I really appreciate this MisterE, thanks.
Yeah it was a weird bug, I'm not sure 100% its resolved but I havent been able to recreate it in the last few hours. So hopefully its stable.
Anyways, the good that came out of this: a new world, and I've created a script to automate backups on a weekly basis. I may look into a daily backup system that uses incremental backups or differential in the future. For now weekly should be OK.
I also took this world re-generation to remove some unnecessary items. I think almost 20% of blocks, or 400 items were removed. Loading times are improved quite a bit. Mainly Ethereal, Clothing, and some MTG_plus