This is a major headache to do in filemaker 5 as it doesn't provide direct access to external data source references like you can with current versions of filemaker.
I'd disconnect your old server, open the files with a full access password. Each time your files attempt to access the original server, you'll get a message popping up telling you that filemaker can't find the file. Each time, you can use open remote to find the copy of the file on the new server to open and connect. That should fix the connection for that one instance where it needs to be updated.
The really tedious aspect of this, is that you will need to exhaustively test your system and fix each such broken reference one at a time and there's no real way to know when you've finally tracked down and fixed all the broken references.
Older versions of filemaker such as filemaker 5 did a really poor job of managing external file references. Converting an older file of this type to filemaker 11 and and then using Manage | External Data sources... typically reveals an amazingly awful tangle of file references.
Perfect thank you for the quick response, looks like i have some initial work to do here but i just needed to know how the server would react.
Thank you for putting me on the right path :)