I usually just loose my presets, but I did have one multi effect that seemed to get a little squirrelly after the battery died and I replaced it. Certain functions got lost. For instance, I could not change certain global parameters and for some reason a few, seemingly random factory presets were permananetly "safe locked" against overwrites - even when I unlocked them in the utility menu - so that I could NEVER again overwrite them. (?)
I can't be sure, however, that this is related to the backup battery dieing and being exchanged. It could be a bug in the unit, just something I noticed when I wet to reprogram the thing after replacing the backup battery.
Nevertheless, that experience would not - and has not - disuaded me from changing out backup batteries when they need to be changed.