I want to add something here, in case there's a misunderstanding.
Regardless of the symptoms that were reported, there is NO WAY THAT THE PCM GOT REPROGRAMMED by this malfunction. The displays in the Gryphon were possibly set back to the default ones, but that does not effect the tune in the truck. The OP could have simply driven the truck as usual. AND he probably should not have tried to reprogram the truck! The reprogramming process needs a healthy battery to complete properly and he actually risked being stranded with a "partially programmed" PCM by doing what he did.
Dead or dying batteries will not effect the program in the PCM - period! The only way the program can be changed is with a reflashing tool, like the dealer has, or with the Gryphon, that can supply 18 volts to command the PCM to accept the new program.
So, if by chance the OP opened the Custom Options Menu to "check" things like the Gear Ratio, Shift Points and so on,
he was actually initiating a new programming session!
DON'T DO THIS! The Custom Options Menu is not there to "check" anything! It is there for you to make small changes to a tune. Any value you "see" in the Custom Options Menu is likely a "default" value or a simple "placeholder" that is meaningless
unless you have chosen the "Reload Previous Settings" option as the first step after opening that menu.
And, one more thing. Looking at the output of the alternator with the engine running tells you little or nothing about the health of your battery. If the battery is
badly shorted internally the charging voltage will probably be low, but if that's the case, the battery will probably not start the truck either. A "load test" will usually detect a failing battery but sometimes that even gives a "false good" diagnosis.
Of course, if I'm wrong on any of this, people will jump all over me, so, here's their chance!
PS: A lightning stroke or the EMP from a nuclear blast MIGHT "fry" the PCM, which technically could be considered a "reprogram".
- Jack