I have searched for information on this and can't find anything. Was wondering if someone can shed some light:
Say you have mod A that changes a cell in Skyrim. Then you load Mod B AFTER mod A and mod B changes the cell back to Default Skyrim (i.e. the end result is there is no change to the cell). Mod B does have an identical to master record but because you are loading MOD A before it TES5Edit does not report it and the record is not cleaned. This may be a good or a bad thing although it can be resolved by load order.
However (and this is my real question):
Say you have Mod B loaded in your load order. You run TES5Edit and it reports it as identical to master and you clean it, the change to the cell is removed. But, I play Skyrim, a new mod comes out I want to try. I decide I am going to start a new Character from the beginning and put this new mod in my load order (we will call it Mod A). I load Mod A before Mod B. Mod A changes the cell, it would have been reverted back to original Skyrim if I had left Mod B alone, but because I cleaned Mod B it won't be reverted back and I probably would never know because I'm not exactly keeping a list of all the changes made by Tes5Edit when I clean my mods.
So, besides keeping a copy of the original mod and re-cleaning each mod every time I introduce a new mod, is there any other way around this?