I have done this a lot while testing. tar up your wallets folder and put it in ~/Documents or something. Then you can be a bit more cavalier about your deletes. The client will create everything is needs and use the wallets/default directory if it's there and create it if not.
If you want to be sure tar it up and put it somewhere else (btsx_wallets.tar) then delete the entire Bitshares\ X directory, luanch the new client, exit the client, put your wallets directory back, launch the client and wait for the chain to sync.