Batman: Arkham Origins 2xDVD5 [SP only] / 3xDVD5 [SP+MP] [CIUv2 + lzma + 1lang]

[BAMsE]

Proper preprocess file no more deletes anything, just replacing compressed files with uncompressed. So if there is no uncompressed Playable_BmCash_SF.upk it will stay as is.
But... Why do you install DLC if you plan to not include it in conversion? The DLC makes changes in game files, probably in exe too, so it's highly probable you will have more problems with it.
Just make fresh install, update it to v20131204 or even higher (just compare fresh with updated and report differences - I'll try to make bunch of new files for you)

EDIT:
Excellent tool for comparing two folders (missing files, sizes, dates etc) is Total Commander: Commands ---> Synchronize Dirs...