I think the problem is that FileMaker Pro and more importantly FileMaker Go doesn't fully close a related file even when doing so from a blank layout with no references to the related file.
This is an important issue when using FileMakerGo to sync data between server files and local database app!
Quote from archives:
"May 29, 2011 10:18 PM
Cannot close file that was opened via reference
Originally Posted By: Christopher Gauntt, firstname.lastname@example.org
Closing a related file doesn't actually "close" the file, it reduces it to "hidden" status.
The other problem:
The documented solution according to the FileMaker help files is to make sure you are on a layout with no related fields, and then close the external file. THIS DOES NOT WORK!
The issue appears to be resolved by re-creating from scratch a specific layout which presumedly was damaged in some manner. (This wasn't picked up by FileMaker's Recover process.)
Also interesting to note that FileMaker Go appears to want to "hang on" to related files even after using script steps such as "Close File" and "Exit Application".