Hey Mikky,
When you are saying you Print from your iPad to a PaperCut queue, do you mean via Mobility Print? If so are you using mDNS or DNS and have there been any changes in the Network, there are some changes that can affect Mac Devices only.
Which Version of PaperCut are you currently running? Is your Primary and your Secondary Server on the same Version?
As you are printing to an MFD I assume you are using PaperCut MF, did you try to contact your Reseller? They can be usually quite helpful with troubleshooting.
Cheers,
Nora