A hotfix has been put out that should fix the majority of issues introducted with converting saves in the original patch 1.04.
For those who would like to know what happened, an extension that looked at your computer's name (was left over from leaderboards) interfered with the new save system and would, for some people, delete in-game achivements or cosmetics. This extension didn't do anything in the current game, and has no purpose anymore so it's been removed and this issue should no longer occur.
If you backed up your save, you can use the backups and the data should still be fine. If you did not, you may be able to use a system restore point to get your old saves back. Because the data is deleted, we cannot restore it.
If you can prove some of the cosmetics you had through steam pictures or achivements previous to the patch I can restore these on a case-by-case basis, but there is no global patch we can put out for this.
We're incredibly sorry for anyone this might have effected, and will try to fix and problems this may have caused.
If you are still experiencing problems please post on the steam forums.
EDIT: There was another issue with the game flashing your save information for a second then going back to the menu, this should be fixed too.