Deleted the world and had no further issues.
Apologies in advance if this is in anyway incomplete.
So I don't entirely know how I would go about explaining my issue. The issue is when removing a mod which adds any block( e.g A modded ore), then going through /fml confirm process the server tries to make a back up of the world. That is where the issue starts; Forge fails to make a world backup (that is also sometimes a fully corrupted .zip file) then forces an immediate stop of the sever(essentially crashing).
Well here is everything I have to help.
Fml-server-latest
https://gist.github.com/TripOptic/e4044a885f6aa1f8e691266b7193c5a5
Fml-client-latest
https://gist.github.com/TripOptic/4388a6156402cce59d7f95c978873fc7
Picture of server console
Side note: AromaBackup has the same issue creating auto saves(doesn't crash just fails).