sorry - I may have misunderstood, are you “reloading patches back on” by putting the .zip files back on (either usb drive or sd card) and THEN unzipping them? From your post I got the impression you were unzipping them first. If you could be more specific about what’s happening you might be able to get more help from people more knowledgable than I am.
If your sd card got erased, did you re-flash the card with the latest organelle os (3.1)? How to: Start over?