So recently I was trying to back up my saves for a format that I didnt end up doing (not using cloud saves) and for whatever reason I lost my entire transfer stash and 3 levels worth of progress (which included some significant upgrades in gear)... Also im no longer at the same point in the game as the person i was playing with. Is there anything I can do to recover that?

This kind of progress loss should only happen if you had 2 savegamelocations and switched them or if moving saves in&out for backupreasons and mixed up the saves. If you changed the savelocations or moved the saves just find the latest save and copy them in the original folder for savegames.

If it happen through same strange bug..you can only "restore" your char via Hexedit or GD-Stash that has some features that allow editing your save

Edit:
http://www.grimdawn.com/forums/showthread.php?t=23414 (the Link to GD-Stash)

Also appears to happen if you have a character in Main and copy them via Link Shell extension to the User folder for use in Custom games. My Demollitionist did this. I'd collect stuff, have full inventory, play through a quest and gain experience. I even gained a level. Switch back to Main Menu, shut down the game and the cloud saves apparantly synced, open the character next time, nothing. Happened several times. Try playing the characxter from the Main menu, That appears to work. Another point, tried a character in the custom menu with no link to the Main menu. Had no problems. Hope this helps. Another point on Symbolic links (Shell Link Extension program) If you uninstall and reinstall this, your earlier links are messed up. Perhaps avoid this or find another method to import Main Characters to the User folder.