A create contraption destoryed my grave. It picked up most of the items from it, but it didn't get the stuff in weird slots like my backpack, so i looked into restoring it from a backup. Upon testing, using /yigd grave and then restoring from backup worked, but now many of the items were duped so i decided to use /clear to wipe my inventory and restore fresh from the grave backup.

However, after running the /clear command, the grave backup is now empty. The XP levels are still present but it now says 0 items. I checked with another grave, and this is happened after running the /clear command with items from that grave in my inventory, NOT when running the restore command.

Any idea of what could have happened / ideas to fix?

I think I know what happened, and I'm sorry this has inconvenienced you. Pretty sure this is because the items are shared between the backup, and when they are retrieved. It's pretty easy to fix though.
I can't help you get your items back unfortunately, but I can try to prevent this from happening in future updates of the mod. I'll let you know when I update.