I am having problems with importing lxo files, and would like to disable the import (I have a whole bunch of old source lxo files as backup for the fbx files I use). I have to keep my lxo files, to keep information for baking and such, I would hate to move all my files out of the project folder, but I am suspecting that this the only solution?
Open the old files and save them back out from 501? If that's not an option then yeah - you should definitely separate the source files from your final "build files." Only cases where the working file is the same as your production file should it live in /Assets. e.g. PSD, Blend, LXO(5) etc.