Hmmm I suppose the surest way would be to delete the VanillaMod folder completely and then look for hidden related things you delete as well. Then reinstall it.
Of course you can just delete any hidden file instead as there should be none in VanillaMod. Actually, I imagine you started from 0.93 right? In that case, just delete each and every file you can also find in the 0.93to0.93b folder and then move them back from the downloaded archive.
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