We need to get someone more knowledgeable about ITMs in here, because I swear I remember reading a post by Arthmoor saying that it's almost impossible for removed ITMs to cause problems.
EDIT: This is the post I was thinking of: http://forums.bethso...st__p__21676083
I think it works like this:
1) Mod A relies on the vanilla game's Object 1, whilst modifying Objects 2 and 3.
2) Mod B modifies Objects 6-8 and Object 1.
3) Mod A is loaded AFTER mod B.
4) Both mods are cleaned of ITMs and UDRs.
Assuming that Mod A is cleaned with TES5Edit and is lower in the load order, Object 1 will be overwritten by Mod B, since the Identical to Master record was previously removed from Mod A.
So now Mod A relies on an incompatible record from Mod B.
But this is a mod incompatibility and what is required here is a compatibility patch. I still can't think of any "Objects" or records for that matter that would conflict this way.
I'm also sure there's a better way of making sure the vanilla records are used when a mod requires that.