Probably the best to flash back to stock then, if they update you, you get the latest stock tune saved when you put your tune back......so you have it if you trade/sell.
The advice below is sound... however, When Flash memory (in your ECU) is erased it leaves a"ghost" that Ford engineers can find if there is a major failure and they look. For any computer the data is just taken off the directory and may or may not be overwritten. The regular ODBII machines can tell how may times the port has been accessed and when, but not why... but tell them you have an MX or you check at Autozone for problems, etc., if they should ask.
