diff --git a/Orm/Xtensive.Orm.Tests/Issues/IssueJira0796_IgnoreHintPathGetsInvalid.cs b/Orm/Xtensive.Orm.Tests/Issues/IssueJira0796_IgnoreHintPathGetsInvalid.cs
new file mode 100644
index 0000000000..7397ea19cc
--- /dev/null
+++ b/Orm/Xtensive.Orm.Tests/Issues/IssueJira0796_IgnoreHintPathGetsInvalid.cs
@@ -0,0 +1,123 @@
+// Copyright (C) 2020 Xtensive LLC.
+// This code is distributed under MIT license terms.
+// See the License.txt file in the project root for more information.
+// Created by: Alexey Kulakov
+// Created:    2020.03.04
+
+using NUnit.Framework;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Reflection;
+using System.Text;
+using Xtensive.Orm.Configuration;
+using Xtensive.Orm.Tests.Issues.IssueJira0796_IgnoreHintPathGetsInvalidModel;
+using Xtensive.Orm.Validation;
+using Xtensive.Sql;
+using Xtensive.Sql.Dml;
+using Xtensive.Caching;
+using Xtensive.Orm.Upgrade;
+using Xtensive.Modelling.Comparison.Hints;
+using Xtensive.Orm.Upgrade.Model;
+using Xtensive.Orm.Services;
+
+namespace Xtensive.Orm.Tests.Issues
+{
+  [TestFixture]
+  public class IssueJira0796_IgnoreHintPathGetsInvalid
+  {
+    private const string CreateIndexQuery = @"
+      CREATE NONCLUSTERED INDEX [custom_NonClusteredIndex-20200304-164347] ON [dbo].[SomeEntity2] (
+        [FirstName] ASC,
+        [LastName] ASC)
+      WITH (PAD_INDEX = OFF, STATISTICS_NORECOMPUTE = OFF, SORT_IN_TEMPDB = OFF, 
+        DROP_EXISTING = OFF, ONLINE = OFF, ALLOW_ROW_LOCKS = ON, ALLOW_PAGE_LOCKS = ON)";
+
+    [Test]
+    public void MainTest()
+    {
+      Require.ProviderIs(StorageProvider.SqlServer);
+
+      var configuration = DomainConfigurationFactory.Create();
+      configuration.UpgradeMode = DomainUpgradeMode.Recreate;
+      configuration.Types.Register(typeof (SomeEntity1));
+      configuration.Types.Register(typeof (SomeEntity2));
+
+      using (var domain = Domain.Build(configuration))
+      using (var session = domain.OpenSession())
+      using (var transaction = session.OpenTransaction()) {
+        var accessor = session.Services.Get<DirectSqlAccessor>();
+        using (var command = accessor.CreateCommand()) {
+          command.CommandText = CreateIndexQuery;
+          _ = command.ExecuteNonQuery();
+        }
+        transaction.Complete();
+      }
+
+      configuration = DomainConfigurationFactory.Create();
+      configuration.UpgradeMode = DomainUpgradeMode.Perform;
+      configuration.Types.Register(typeof(SomeEntity1));
+      configuration.Types.Register(typeof(CustomUpgradeHandler));
+
+      Assert.DoesNotThrow(() => Domain.Build(configuration).Dispose());
+    }
+  }
+}
+
+namespace Xtensive.Orm.Tests.Issues.IssueJira0796_IgnoreHintPathGetsInvalidModel
+{
+  [HierarchyRoot]
+  public class SomeEntity1 : Entity
+  {
+    [Field, Key]
+    public int Id { get; set; }
+
+    [Field]
+    public string FirstName { get; set; }
+
+    [Field]
+    public string LastName { get; set; }
+  }
+
+  [HierarchyRoot]
+  public class SomeEntity2 : Entity
+  {
+    [Field, Key]
+    public int Id { get; set; }
+
+    [Field]
+    public string FirstName { get; set; }
+
+    [Field]
+    public string LastName { get; set; }
+  }
+
+  public class CustomUpgradeHandler : UpgradeHandler
+  {
+    private class KeepCustomIndicesMarkerHint : Hint
+    {
+      public override IEnumerable<HintTarget> GetTargets() => Enumerable.Empty<HintTarget>();
+    }
+
+    private const string CustomIndexPrefix = "custom_";
+
+    public override void OnSchemaReady()
+    {
+      if (UpgradeContext.Stage == UpgradeStage.Upgrading) {
+        var schemaHints = UpgradeContext.SchemaHints;
+        var storageModel = (StorageModel) schemaHints.SourceModel;
+
+        foreach (var table in storageModel.Tables) {
+          foreach (var index in table.SecondaryIndexes) {
+            var name = index.Name;
+            if (!name.StartsWith(CustomIndexPrefix)) {
+              continue;
+            }
+            var ignoreHint = new IgnoreHint(index.Path);
+            schemaHints.Add(ignoreHint);
+          }
+        }
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/Orm/Xtensive.Orm/Modelling/Comparison/Upgrader.cs b/Orm/Xtensive.Orm/Modelling/Comparison/Upgrader.cs
index d0b6336c34..2ee5dbe25d 100644
--- a/Orm/Xtensive.Orm/Modelling/Comparison/Upgrader.cs
+++ b/Orm/Xtensive.Orm/Modelling/Comparison/Upgrader.cs
@@ -1,6 +1,6 @@
-// Copyright (C) 2003-2010 Xtensive LLC.
-// All rights reserved.
-// For conditions of distribution and use, see license.
+// Copyright (C) 2009-2020 Xtensive LLC.
+// This code is distributed under MIT license terms.
+// See the License.txt file in the project root for more information.
 // Created by: Alex Yakunin
 // Created:    2009.04.07
 
@@ -122,20 +122,23 @@ public ReadOnlyList<NodeAction> GetUpgradeSequence(Difference difference, HintSe
     {
       ArgumentValidator.EnsureArgumentNotNull(hints, "hints");
       ArgumentValidator.EnsureArgumentNotNull(comparer, "comparer");
-      if (difference == null)
+      if (difference == null) {
         return new ReadOnlyList<NodeAction>(Enumerable.Empty<NodeAction>().ToList());
+      }
 
       TemporaryRenames = new Dictionary<string, Node>(StringComparer.OrdinalIgnoreCase);
       SourceModel = (IModel) difference.Source;
       TargetModel = (IModel) difference.Target;
       Hints = hints ?? new HintSet(SourceModel, TargetModel);
       Comparer = comparer;
-      if (Hints.SourceModel!=SourceModel)
+      if (Hints.SourceModel != SourceModel) {
         throw new ArgumentOutOfRangeException("hints.SourceModel");
-      if (Hints.TargetModel!=TargetModel)
+      }
+      if (Hints.TargetModel != TargetModel) {
         throw new ArgumentOutOfRangeException("hints.TargetModel");
+      }
 
-      CurrentModel = (IModel)SourceModel.Clone(null, SourceModel.Name);
+      CurrentModel = (IModel) SourceModel.Clone(null, SourceModel.Name);
       Difference = difference;
       var previous = currentAsync.Value;
       currentAsync.Value = this;
@@ -152,15 +155,17 @@ public ReadOnlyList<NodeAction> GetUpgradeSequence(Difference difference, HintSe
           ProcessStage(UpgradeStage.Cleanup, actions);
 
           var validationHints = new HintSet(CurrentModel, TargetModel);
-          Hints.OfType<IgnoreHint>().ForEach(validationHints.Add);
+          Hints.OfType<IgnoreHint>()
+            .Where(h => CurrentModel.Resolve(h.Path, false) != null && SourceModel.Resolve(h.Path, false) != null)
+            .ForEach(validationHints.Add);
           var diff = comparer.Compare(CurrentModel, TargetModel, validationHints);
-          if (diff!=null) {
+          if (diff != null) {
             CoreLog.InfoRegion(Strings.LogAutomaticUpgradeSequenceValidation);
             CoreLog.Info(Strings.LogValidationFailed);
             CoreLog.Info(Strings.LogItemFormat, Strings.Difference);
             CoreLog.Info("{0}", diff);
-            CoreLog.Info(Strings.LogItemFormat+"\r\n{1}", Strings.UpgradeSequence, 
-              new ActionSequence() {actions});
+            CoreLog.Info(Strings.LogItemFormat + "\r\n{1}", Strings.UpgradeSequence,
+              new ActionSequence() { actions });
             CoreLog.Info(Strings.LogItemFormat, Strings.ExpectedTargetModel);
             TargetModel.Dump();
             CoreLog.Info(Strings.LogItemFormat, Strings.ActualTargetModel);