A.omod
B.omod
C.omod
1) I install mode A. No problems.
2) Now I install mod B. Mod B overwrites 2 files from mod A; 1.nif and 2.nif.
3) Moving on to mod C. Mod C overwrites 1.nif
Now here's the problem... I decide I don't like mod C, so I deactivate mod C from OBMM. I'm screwed, because even if I deactivate mod C, the 1.nif from mod C will remain there, messing up mod B's install.
Now this may not seem like a big deal, but this is just an example. A real-life mod setup consists of .omods of unofficial patches, Qarl's texture pack, body mods, texture mods, who all overwrite the hell out of each other.

1) I install unofficial patches
2) I install Qarl's Redimized. Some files from the UOP will be overwritten.
3) I install Animated Window Lighting System. The mod overwrites files that both exist in Qarl's and the UOP.
In the above example, if I decide I don't like AWLS, I basically have to uninstall everything and start from scratch (vanilla) because a lot of files were overwritten in the process and keeping track is hard.
What I want IDEALLY is basically... a mod install system that makes backups of the overwritten files, and upon deactivating the latest mod in the install chain, files that were overwritten by the latest mod will be restored to the previous mod's version. Using my first example above (mods A, B and C):
1) I install mod A.
2) I install mod B. 1.nif and 2.nif from mod A is backed up, then gets overwritten with mod B's versions of the files.
3) I install mod C. 1.nif from mod B gets backed up, then overwrites that file with mod C's version.
4) I decide I don't like mod C. I uninstall it - 1.nif gets deleted, then the 1.nif from mod B that was backed up earlier is restored. Essentially making it as if I never installed mod C at all, restoring my mod setup to whatever it was before I installed mod C.
I will be honest and admit that I've never touhed BAIN before this because it seems kinda intimidating at first... I want to, but my time is really limited these days (I'm a full time sound engineer, I don't have as much gaming time as I used to when I was younger), you can imagine how much time modding can take out of you, especially for the bigger mods that change hundreds of files... installing/reinstalling from scratch is no fun.
So does BAIN work the way I *think* it does? I am willing to learn if it'll help me save time (and headaches) during my modding adventures.
Thanks for your time.