Make a new Savefile, go to your Stats screen and press Alt+F2. This syncs that savefile with your Achievements and unlocks everything you had. It will display Challenges as not completed tho, but you will have the items the challenges unlocked. (Trance
(Above is what exactly i did with my Binding of Isaac game).
now you can go to your stats screen and press Alt+f2 and it'll restore everything but if you can not see your character achievements or items, DON'T WORRY they're there its just takes time to load. Another thing you could do is refresh the game (get out and relog back on) it should all be there. This just happened to my boyfriend and he finished the entire game. but we did figure out if you just start the round (enter in and just mess around with the character a little bit) and you shall get all of your achievements and items reloaded.