Continue to work with the original return. If payments were made with the extension, they will only be in the software as memo, so you will need to enter the actual amounts paid. It is in the same general area as estimate tax payments. The efile extension data is tied to the client, so keep it intact and do not make a copy. As stated above, print a pdf copy of the return and keep it offline. Keep pdf copies of ALL returns you have finished, as PTO has previous pulled the rug out on old returns, so the pdf is the only record available.