So, after chatting for a while with the guys over at Unreal Engine channel on Discord, we figured to move all the assets from the original project to a new and clean one. That seemed to resolve the issue with packaging, however the controls didn't work correctly. We fixed that by just copy-pasting DafultInput.ini from the original project to the new directory ([NAME OF THE PROJECT]>Config). In case anyone in the future has the same problem, hope this helps. Cheers!