Did the factory patches change...

[ARNK]

With the recent versions? The patch list?

[extempo]

Nope, the factory programs are still as they are listed here: https://www.sequential.com/downloads/pro2/programs/Pro_2_Programs_List.pdf

Program memory is separate from where the OS lives, so updating your OS never affects your programs. It's still not a bad idea to backup your programs prior to an OS update, though. I tend to do backups prior to updates out of convenience, since I'm already getting set up to do sysex transfers.