diff --git a/docs/servere-og-databaser.md b/docs/servere-og-databaser.md
index 6a807b1..9df5fe1 100644
--- a/docs/servere-og-databaser.md
+++ b/docs/servere-og-databaser.md
@@ -47,7 +47,7 @@ AX-fund sendes som standard **ikke** til SQLInsight Hub. Kolonnen *AX-fund til S
 
 ## Servere fra konfigurationsfilen
 
-Servere under `SQLInsight:Instances` i agentens `appsettings.json` eller `sqlinsight.ini` (fx `MONITOR_SERVER` fra installeren) virker som før: ved hver start spejler agenten dem ind i repositoriet, hvor de vises som **fra konfigurationsfil**. Forbindelsen (og en eventuel adgangskode) bliver i filen; den kopieres aldrig til repositoriet. Her kan de sættes på pause, og databaserne kan vælges, men de rettes og fjernes i filen. Som standard overvåges alle deres databaser, også nye, præcis som i 1.2. Bruges samme navn både i filen og i webbrugerfladen, vinder filen.
+Servere under `SQLInsight:Instances` i agentens `appsettings.json` eller `sqlinsight.ini` (fx `MONITOR_SERVER` fra installeren) virker som før: ved hver start spejler agenten dem ind i repositoriet, hvor de vises som **fra konfigurationsfil**. Forbindelsen (og en eventuel adgangskode) bliver i filen; den kopieres aldrig til repositoriet. Her kan de sættes på pause, og databaserne kan vælges, men de rettes og fjernes i filen. Fjernes en server fra filen, markeres den som fjernet ved agentens næste start (det indsamlede bevares); sættes den i filen igen, får den sin pause og sine databasevalg tilbage. Som standard overvåges alle deres databaser, også nye, præcis som i 1.2. Bruges samme navn både i filen og i webbrugerfladen, vinder filen.
 
 Ændringer i webbrugerfladen (nye servere, pause, fjernelse, valg af databaser) bruges af agenten inden for et minut, uden genstart. Ændringer i konfigurationsfilen kræver stadig en genstart af agenten.
 
diff --git a/src/SQLInsight.Repository/InsightRepository.InstanceConfiguration.cs b/src/SQLInsight.Repository/InsightRepository.InstanceConfiguration.cs
index 8c6a60d..1394e18 100644
--- a/src/SQLInsight.Repository/InsightRepository.InstanceConfiguration.cs
+++ b/src/SQLInsight.Repository/InsightRepository.InstanceConfiguration.cs
@@ -349,8 +349,9 @@ public sealed partial class InsightRepository
 
     /// <summary>
     /// Brings the ConfigFile rows in step with SQLInsight:Instances in the agent's configuration: new ones are added
-    /// (monitoring every database, as before 1.3), changed ones updated, and ones no longer in the file deleted. A Web
-    /// instance with the same name gives way to the file. Returns the ids by name.
+    /// (monitoring every database, as before 1.3), changed ones updated, and ones no longer in the file marked removed
+    /// (RemovedAt, like a removed Web instance), so their pause and database choices come back with them if they are put
+    /// back in the file. A Web instance with the same name gives way to the file. Returns the ids by name.
     /// </summary>
     public async Task<IReadOnlyDictionary<string, int>> SyncConfigFileInstancesAsync(IReadOnlyList<ConfigFileInstance> instances, DateTimeOffset now,
         CancellationToken cancellationToken = default)
@@ -361,27 +362,36 @@ public sealed partial class InsightRepository
         var at = Utc(now);
         var names = instances.Select(i => i.Name).ToList();
         await connection.ExecuteAsync("""
-            DELETE FROM insight.ConfiguredInstances
-            WHERE Source = 'ConfigFile' AND Name NOT IN (SELECT value FROM OPENJSON(@names));
+            UPDATE insight.ConfiguredInstances
+            SET RemovedAt = @at, RemovedBy = N'SQLInsight Agent: ikke længere i konfigurationsfilen', UpdatedAt = @at, UpdatedBy = N'SQLInsight Agent (konfigurationsfil)'
+            WHERE Source = 'ConfigFile' AND RemovedAt IS NULL AND Name NOT IN (SELECT value FROM OPENJSON(@names));
             UPDATE insight.ConfiguredInstances SET RemovedAt = @at, RemovedBy = N'SQLInsight Agent: navnet bruges i konfigurationsfilen'
             WHERE Source = 'Web' AND RemovedAt IS NULL AND Name IN (SELECT value FROM OPENJSON(@names));
             """, new { names = System.Text.Json.JsonSerializer.Serialize(names), at }, transaction).ConfigureAwait(false);
         var ids = new Dictionary<string, int>(StringComparer.OrdinalIgnoreCase);
         foreach (var instance in instances)
         {
+            // At most one ConfigFile row per name: a removed one is brought back (with its choices) rather than a new one added.
             ids[instance.Name] = await connection.ExecuteScalarAsync<int>("""
-                UPDATE insight.ConfiguredInstances
-                SET Server = @Server, Port = NULL, Authentication = @Authentication, UserName = @UserName, Encryption = @Encryption,
-                    TrustServerCertificate = @TrustServerCertificate, PasswordCipher = NULL, PasswordKeyId = NULL
-                WHERE Source = 'ConfigFile' AND Name = @Name
-                  AND (Server <> @Server OR Authentication <> @Authentication OR ISNULL(UserName, N'') <> ISNULL(@UserName, N'')
-                       OR Encryption <> @Encryption OR TrustServerCertificate <> @TrustServerCertificate OR Port IS NOT NULL);
-                IF NOT EXISTS (SELECT 1 FROM insight.ConfiguredInstances WHERE Source = 'ConfigFile' AND Name = @Name)
+                DECLARE @id int = (SELECT TOP (1) ConfiguredInstanceId FROM insight.ConfiguredInstances
+                                   WHERE Source = 'ConfigFile' AND Name = @Name ORDER BY CASE WHEN RemovedAt IS NULL THEN 0 ELSE 1 END, ConfiguredInstanceId DESC);
+                IF @id IS NULL
+                BEGIN
                     INSERT insight.ConfiguredInstances (Name, Server, Authentication, UserName, Encryption, TrustServerCertificate, Source, Paused,
                         MonitorNewDatabases, CreatedAt, CreatedBy, UpdatedAt, UpdatedBy)
                     VALUES (@Name, @Server, @Authentication, @UserName, @Encryption, @TrustServerCertificate, 'ConfigFile', 0, 1,
                         @at, N'SQLInsight Agent (konfigurationsfil)', @at, N'SQLInsight Agent (konfigurationsfil)');
-                SELECT ConfiguredInstanceId FROM insight.ConfiguredInstances WHERE Source = 'ConfigFile' AND Name = @Name;
+                    SET @id = SCOPE_IDENTITY();
+                END
+                ELSE
+                    UPDATE insight.ConfiguredInstances
+                    SET Server = @Server, Port = NULL, Authentication = @Authentication, UserName = @UserName, Encryption = @Encryption,
+                        TrustServerCertificate = @TrustServerCertificate, PasswordCipher = NULL, PasswordKeyId = NULL, RemovedAt = NULL, RemovedBy = NULL,
+                        UpdatedAt = @at, UpdatedBy = N'SQLInsight Agent (konfigurationsfil)'
+                    WHERE ConfiguredInstanceId = @id
+                      AND (RemovedAt IS NOT NULL OR Server <> @Server OR Authentication <> @Authentication OR ISNULL(UserName, N'') <> ISNULL(@UserName, N'')
+                           OR Encryption <> @Encryption OR TrustServerCertificate <> @TrustServerCertificate OR Port IS NOT NULL);
+                SELECT @id;
                 """, new { instance.Name, instance.Server, instance.Authentication, instance.UserName, instance.Encryption, instance.TrustServerCertificate, at },
                 transaction).ConfigureAwait(false);
         }
diff --git a/src/SQLInsight.Repository/Migrations/0016_instance_configuration.sql b/src/SQLInsight.Repository/Migrations/0016_instance_configuration.sql
index 25a9074..689492f 100644
--- a/src/SQLInsight.Repository/Migrations/0016_instance_configuration.sql
+++ b/src/SQLInsight.Repository/Migrations/0016_instance_configuration.sql
@@ -37,9 +37,10 @@ CREATE TABLE insight.ConfiguredInstances
     RemovedBy              nvarchar(256) NULL,
     LastDiscoveryAt        datetime2(0) NULL,
     LastDiscoveryError     nvarchar(1000) NULL,
-    CredentialError        nvarchar(1000) NULL,
-    /* An instance from the configuration file is removed by removing it from the file. */
-    CONSTRAINT CK_ConfiguredInstances_RemoveWeb CHECK (Source = 'Web' OR RemovedAt IS NULL)
+    CredentialError        nvarchar(1000) NULL
+    /* An instance from the configuration file is removed by removing it from the file: the agent then sets RemovedAt
+       (like a removed Web instance, so its history, pause and database choices are kept), and clears it again if the
+       instance comes back in the file. */
 );
 CREATE UNIQUE INDEX UQ_ConfiguredInstances_Name ON insight.ConfiguredInstances (Name) WHERE RemovedAt IS NULL;
 
diff --git a/tests/SQLInsight.IntegrationTests/InstanceConfigurationRepositoryTests.cs b/tests/SQLInsight.IntegrationTests/InstanceConfigurationRepositoryTests.cs
index 09eb7d9..c0e0a6f 100644
--- a/tests/SQLInsight.IntegrationTests/InstanceConfigurationRepositoryTests.cs
+++ b/tests/SQLInsight.IntegrationTests/InstanceConfigurationRepositoryTests.cs
@@ -68,7 +68,6 @@ public class InstanceConfigurationRepositoryTests(SqlServerFixture sql) : IAsync
         await Assert.ThrowsAsync<SqlException>(() => web.CompleteAgentRequestAsync(request, true, "{}", null, now));
         await Assert.ThrowsAsync<SqlException>(() => web.SaveDiscoveredDatabasesAsync(id, [Db("Sales")], now));
         await Assert.ThrowsAsync<SqlException>(() => web.PublishAgentKeyAsync(new AgentKeyRow { KeyId = "x", PublicKey = [1], MachineName = "m", ServiceAccount = "a", CreatedAt = DateTime.UtcNow, LastSeenAt = DateTime.UtcNow }));
-        await Assert.ThrowsAsync<SqlException>(() => web.SyncConfigFileInstancesAsync([], now));
         await Assert.ThrowsAsync<SqlException>(() => ExecuteAsWebAsync($"DELETE FROM insight.ConfiguredInstances WHERE ConfiguredInstanceId = {id}"));
         await Assert.ThrowsAsync<SqlException>(() => ExecuteAsWebAsync($"UPDATE insight.ConfiguredInstances SET Source = 'ConfigFile' WHERE ConfiguredInstanceId = {id}"));
         await Assert.ThrowsAsync<SqlException>(() => ExecuteAsWebAsync($"UPDATE insight.ConfiguredInstances SET Name = N'x' WHERE ConfiguredInstanceId = {id}"));
@@ -142,11 +141,21 @@ public class InstanceConfigurationRepositoryTests(SqlServerFixture sql) : IAsync
             new ConfiguredInstanceChange("evil", null, "Windows", null, null, null, false, "Mandatory", false), null, now));
         Assert.Equal(ConfigurationChangeOutcome.Changed, await _repository.SetInstancePausedAsync(ids["prod-sql01"], true, null, now));
 
-        // Started again with one instance changed and one gone: the same row is kept (with its choices), the other deleted.
+        // Started again with one instance changed and one gone: the same row is kept (with its choices), the other marked removed.
         var again = await _repository.SyncConfigFileInstancesAsync([new ConfigFileInstance("prod-sql01", "sql01b", "Windows", null, "Mandatory", false)], now);
         Assert.Equal(ids["prod-sql01"], again["prod-sql01"]);
         var row = Assert.Single(await _repository.GetConfiguredInstancesAsync());
         Assert.Equal(("sql01b", true), (row.Server, row.Paused));
+        Assert.Null(await _repository.GetConfiguredInstanceAsync(ids["prod-sql02"]));
+
+        // Put back in the file: the same row comes back, nothing is lost and no second row is made.
+        var back = await _repository.SyncConfigFileInstancesAsync(
+        [
+            new ConfigFileInstance("prod-sql01", "sql01b", "Windows", null, "Mandatory", false),
+            new ConfigFileInstance("prod-sql02", "sql02", "SqlLogin", "mon", "Optional", true),
+        ], now);
+        Assert.Equal(ids["prod-sql02"], back["prod-sql02"]);
+        Assert.Equal(2, (await _repository.GetConfiguredInstancesAsync()).Count);
     }
 
     [Fact]