Case of folder and file names is the biggest issue when switching OS.
Windows does not care (or fix) if you change the metadata (title and/or Author) Case and leaves the folder 'as was'.
THE BOOK -> The Book
OTOH Linux derived OS does care. resulting in
lost files.
Step 2) after transfer should always run the full
Library Maintenance and fix.

I believe Quality Check PI: Fix has a rename paths tool (have not tried for this case)