This was 100% from AMP backups, I have tested and can confirm, I made a backup with an ATM9 TTS server, reloaded the server, chunks gone, this may just be an issue with my AMP in particular but who knows. I am now using Duplicacy to make backups of the servers and it seems to be working fine, also added the SimpleBackups forge mod to make sure I have enough backups xD.
I only ever use windows file explorer on this server and haven’t had issues before with permissions, and this is over 10 years of messing around with minecraft and servers