Only some people claim that. TesVsnip works fine for me, hasn't broken a thing yet.
But yeah, Version Control is the proper way.
You've been lucky then. TESVSnip doesn't recompress records. It decompresses them just fine, but doesn't compress them again on saving. If you don't flip the compression flag then the game will still expect those records to be compressed.
The more serious issue is that Snip doesn't handle the second layer of compressed records - at all. There is another flag that indicates if there is a compressed sub-record and Snip isn't recognizing that flag right now. I'll have to get this documented and posted up. We are processing the extra compression in Gecko. Not all records have compressed sub-records, so it's possible your mod doesn't have any and that's why you're not seeing a problem.
Oh, and Gecko will offer mod merging as one of the features once we're done.