When running a fm server12 backup routine, is there a way to NOT backup the files that are stored in external containers?

Why would you want that?  External Container data is very much part of your FM file.  And if the data does not change, FMS does not waste time backing up unchanged external files, it just uses hard links.  So there really is no benefit to excluding the data

how do you have filemaker server advanced only save changed external data. my backup, backs up all the external data regardless of when the last time it was changed.

The backup set is always complete (otherwise it would never be a good backup), but under the hood, FMS only spends time and disk space on new and modified container data.  The other data is hard-linked.   For all intents and purposes it does not matter except that it is really fast and efficient.  In Finder / Windows Explorer, each backup is represented as a complete set and you can copy it or zip it and you will always have all the files and data.

 

Very easy to demonstrate if you want me to post screenshots.  I demoed this at Devcon 3-4 years ago.