I don't have a problem with the patch and my AT and AA mod. Even the RSM worked fine.
First thing one should do when modding is record what you modded.
I wouldn't be surprised if they don't teach that in college yet.
I've worked in configuration management and know what a nightmare is.
1) it is more work to adapt your mod to the 1.1 patch
2) you will not get all the benefits from the patch unless you use the same format
3) I disagree with the posts above as vanilla mods to equipment file are effected. Example AT & AA mod
4) Using your record of changes: go into 1.1 and re-update the values in equipment file
5) any custom units should have been coded correctly ie; high id numbers, so they do not conflict with other mods and future patches
6) add custom units at the end of the equipment file
7) add customs sounds to efx and animations at end of file

same with tiles if applicable
9) for other auxiliaries like big units, hero photos, head base, flags.... just copy and paste the mod back into the appropriate file.
10) if you made the mod to be used with GME there should be no problem to copy and paste back into correct location
11) only problem I see is adding the new trait features to any custom units IF applicable
12) for campaigns.. I don't think that function has changed. This area takes allot more of my time so I do not pursue that course.
13) Good Luck and I hope this helps