A filemaker database, previously and happily made into a single runtime, is now under threat of running twice on the same computer using the developer utilities to create two different application names and two different database extensions for both versions (two runtimes, two versions of the master database each with a unique extension). At the moment both run with no obvious script clashes or quirks but this is with very limited testing. I'm on Mac which I hope makes things a lot easier.

Can anyone highlight the potential problems in this scenario and/or suggest ways around this?

[back story: the original database is used for one company name but the accountant has been a pain and insisted that certain records are held in a separate database for another company name.]

If it's a single-file database you should be fine. If it's multiple related files, I'd probably use the Developer Utilities to rename them just to be safer.