It rewrites a new file. "Last session" is ONLY last session. If you remove component A from a fresh source then re-nLite it this time not removing component A (cause it's not there, obviously it can't be removed again), your ini file will be such that using it on a fresh source, component A will NOT be removed. Surprise. For some components, it is easy to manually correct this using successive ini files ("append", like you suggest) for others, it is more complicated.