Thank you for your post.
I am unable to replicate the issue using FileMaker Pro 13.0v1 under Windows 7.
I followed your steps, and after I rename B to C, when I open A, I immediately get an error message "The file "B.fmp12" could not be opened (not found)". When I click OK, an Open File dialog box opens to locate B.fmp12. I click Cancel, and A opens. If I then go to Manage Value Lists, the Value List "From B" is listed, but it does list <File Missing>. (See screen shot below). I am unable to make this crash.
Let me know what other steps I need to take to replicate the issue.