I've never done it myself, but one of my subcontractors is doing it for me.
It should be easy. Just make sure the timers are set up to keep from accidentally chattering the outputs.
Also, make sure you don't have latches or SER points that chatter. Each time they toggle, the position is written to the non-volatile memory. The EEPROM has a finite number of writes (about half a million), and you don't want to max it out.