There is nothing about syncing that changes your passphrase. You can be offline with no copy of the blockchain and encrypt or decrypt you wallet.
I just meant if I actually needed to delete my /.bitcoin/ contents. It re-syncs when that happens, correct? The time it took to sync just made me never want to do that again. lol
But your suggestion worked. Thank you for the response. I will just have to double-check after encrypting next time.