First off thats retarded because any tune will REPLACE the file thats currently in the ecm. The PHP gyphon reprograms the ecm to an earlier file this will become your new stock file. When you tune your truck the SCT downloads the stock files to the sct then loads the new files into the ecm, . Most tunes built by tuners are already flashed back so theres no worries. Who ever fed you that line had no idea what they were talking about.
Its been known that its not really the pcm tuning that matters it the ficm flashes that are the problem. They only recommend that you flashback the ecm when you flashback the ficm because they're both in sync with the same family of strategy. It makes no difference if the two strategy families match.
My recommendations are that you just use the SCT to tune/program the ecm and then have someone tune your FICM (send it in to be flashed or wait for a remote programmer)
For the record, loading tunes that arent the same strategy as what your truck is can be done, people who claim it will lockout the pcm are entirely false. Ive never ran a tune that was the same strategy as my stocker.