I noticed that the managed Entity Remapper supports basically every datatype except Dictionaries. This is because Unity.Properties treats Dictionaries as Read-Only by default (in order to avoid modifying keys).
However, it's safe to modify values in a dictionary during traversal, so it's safe to remap Entity references that are a part of the values.
I've added support for Dictionaries to the Entity Remapper in this PR for our fork of com.unity.entities: https://github.com/Pontoco/com.unity.entities/pull/1
I'll go ahead and file a bug for this. As is, using Entity references in a Dictionary results in corrupted entity referenced, which is quite a bit of a footgun!