Okay, since this is clear now, i need to state the obvoius question: Why would you do that? There is absolutley no reason to do such a thing.
Apart from that, it should work as long as you masterkey file and other files in the m directory are untouched. Does your log contain any ERROR or WARN messages?
I can imagine that during up- or download the data might be slighty altered and therefore you get unauthenticated ciphertext warnings.