System.Data.SQLite.EF6 Entities not found after modifying edmx diagram

I'm using EF6 with System.Data.SQLite 3rd party provider (there is no native support for SQLite in EF6).

I have to add inheritance between two tables. Because I can't do this on database level, I have to modify the .edmx diagram:

1. remove the original connection between the two tables (1:N connection), and replace it with the inharitance
2. rename one of the two tables, because EF automatically generates the name, which is not fit to our naming conventions

After I do this Visual Studio won't see the tables (none of them, nor the tables I have not modified), and I get several errors after build ("The type or namespace '' could not be found." ).

If I undo the changes (revert back to the 1:N connection), and save the diagram and the database model everything works fine again.

What am I missing during the changes?