How to reproduce:
1. Open the attached project("Haven.Unity.zip")
2. Load "UnityBootstrap" scene
2. Enter Play mode
3. Wait a few seconds
4. Press "2"

Expected results: AssertionException not thrown
Actual results: AssertionException is thrown

Reproducible with: 2019.3.2f1, 2020.2.0b2 (0.10.0-preview.6, 0.14.0-preview.19)
Couldn't test with: 2018.4.28f1, 2019.4.13f1, 2020.1.10f1, 2020.2.0b8 (Couldn't downgrade/upgrade, because project is too complicated)

Exception thrown: AssertionException: Assertion failure. Values are not equal. Expected: 0 == 2 UnityEngine.Assertions.Assert.Fail (System.String message, System.String userMessage) (at <9584de3444b542abbb1ad4bb43a7137f>:0) UnityEngine.Assertions.Assert.AreEqual[T] (T expected, T actual, System.String message, System.Collections.Generic.IEqualityComparer`1[T] comparer) (at <9584de3444b542abbb1ad4bb43a7137f>:0) UnityEngine.Assertions.Assert.AreEqual[T] (T expected, T actual, System.String message) (at <9584de3444b542abbb1ad4bb43a7137f>:0) UnityEngine.Assertions.Assert.AreEqual (System.Int32 expected, System.Int32 actual) (at <9584de3444b542abbb1ad4bb43a7137f>:0) Unity.Assertions.Assert.AreEqual (System.Int32 expected, System.Int32 actual) (at Library/PackageCache/com.unity.entities@0.14.0-preview.19/Unity.Entities/Stubs/Unity.Assertions/Assert.cs:141) Unity.Entities.EntityComponentStore.AssertSameEntities (Unity.Entities.EntityComponentStore* rhs, Unity.Entities.EntityComponentStore* lhs) (at Library/PackageCache/com.unity.entities@0.14.0-preview.19/Unity.Entities/EntityComponentStoreDebug.cs:183) Unity.Entities.EntityManager.CopyAndReplaceEntitiesFrom (Unity.Entities.EntityManager srcEntityManager)