@BrechtSchamp
I think I created it from scratch not realising that there are 2 options. I tried to renew the old certificate from identity.apple.com and update that certificate. This didn't work.
I have decided to reset the iPads from scratch. Thanks to iCloud, there won't really be any loss of data. As I can only 1 at a time through iTunes. Is there a way I could reset them in bulk? I don't think configurator would work as it would say that they are managed elsewhere.
I'm backing up the .csr, .pem and token files now, so that should help if this happens again.