This was indeed a serious short coming in older versions. The current version of FileMaker is FileMaker 11 and you can select Manage | External Data Sources... to see a list of each and every data source reference external to the current file. This wasn't an option for 5.5 and I don't know when they added it so you may have it, but I doubt it. It's also now possible to combine multiple tables in the same file which can greatly reduce the number of such external data source references in the first place.
"relative path" does indeed mean that the reference is to a file in the same folder as the current file so that should enable you to avoid issues. As a test, you can rename a file or the folder containing it to see if that produces a "file not found" message when you work with the file.
thank you for the reply, it clears things up a bit. I'm not so much worried about a "File not found" as the master file reaching out to the wrong related file in another folder.
I'd like to upgrade to a new version, but I have six licenss to do adn can't afford that for the present, so I'm stuck with 6.