It doesn't delete them, they should still be around.. the reason why it's not so bad however, is because of the game's development, some flags could be deprecated and so on..
Right click the game in your owned items and click show local files, then navigate to the version you had saves in, the folder .toa-data that shijima mentioned contains your saves files, simple move the folder into the newest version, override in case you've already had the game opened, and your saves are back.
(in some cases, i could imagine this could lead to locking your save out of content though... that happened when potential party member encounters were changed to characters on the map, if you used a save from before that change, you could never encounter those potential party members with that char, and had no other option but to start afresh)