From a quick look (at the example SLN in repo at least) it appears as though all files have been updated but they haven't been removed from the project/sln files.  I expect this is the same situation you will be in as these files were built with the old project, and it now "remembers" the files which have been removed.

Note - If you click the "Show all files" at the top of the solution explorer this will highlight the missing source files with warning / error icons

Option 1: They can be manually removed in Solution Explorer one by one under the Headers / Source files Sections (Right Click > Remove each one)
Option 2: You can (backup and) remove the VCXPROJ and SLN files from the project. Then open VS and use File > Open > Arduino Project, this will then re-scan all headers and only include the valid ones which remain since the major refactor on that repo.

Hopefully that helps resolve the issue with that element of the compilation?