How to I resolve "Reference File is of Older Version" in EPDM?

No, but that would be really neat. Then again, and I haven't had the time to play much with this, but i guess the new "version overwrite" feature in PDM 2017 will also help with this problem. I mean it all depends on the engineering change process, but i can easily see this will help out in these kinds of situations. Unless there is a major change, maybe even a revision, you just overwrite existing version, so the version reference tree is maintained and without warnings. Just be careful, it really does overwrite, there is no going back, except backups.

It still seems like a good idea. Perhaps someone should make this an enhancement request, where a company can select whether to update version reference tree or not upon check-in of a sub part or assembly.

At first I to was concerned about this.  The small yellow circle/exclamation point makes the perfectionist in me cringe.  Then I realized that if the change does not effect the geometry, (like a properties update to correct spelling, a material was forgotten, or something low level) then it really does not matter - which is %99 of the time.  What I struggle more with is that out of date references can come up to date by passing the assembly through a transition that contains an action.  We use a few logical branches in our workflow to control a few variables and sometime an out of date part will get updated and sometimes not depending which part of the logical branch it flows through, and weather that branch contains an action.  Most the time it does not matter - but those circles are painful for my ego...  I am looking forward to version overwrite!