Was actually just thinking about that, or just storing them in both locations or adding a savegame export function...Bleh, people are weird. It was handy being in a persistent folder. Could you think about a toggle for persistent/portable save for a later version.
But for now...it's turning into a more confusing thing (with each update) then it should be, so I'll add it to my list for a bit later...I'm too scared I'll get lynched now if I change it again next update!