Shim,
You are right to be cautious. In general when FIM is packaged up for Dirsync or for SharePoint UPS it is configured through the wizard and any changes made through the MIISClient are subject to be overwritten the next time the wizard is run or an upgrade
is performed. For dirsync there are a few supported exceptions.
AFAIK, SharePoint won't overwrite your settings until the Wizard is run again or you patch SharePoint UPS.
What is your goal?
In FIM once records are joined they don't get un joined if you change the Join criteria (it isn't like a SQL View where changing the Join clause alters which records show up) it will change how things are joined going forward.
So if this is just a need to get over some initial hurdle then it would be safe to add a join rule using that criteria rather than changing the existing join rule and then run some imports and syncs (manually) to get the joins you want and deal with any
duplicate join attempts. Then you could delete your new join rule.