as you can just read above in the first sentence of this page:
Since 0.4, your savegames are in the C:\Users\"name"\AppData\Local\MANTIS\User Data\Default folder. You cannot use your old saves from previous versions with this update!
This means you need at least 0.4.7 in order to be able to use old saves. and overwriting the game folder does not matter since the save data is stored in a different location