I understand that it will get blown away and that manually editing it was the wrong thing to do but I was missing something in the GUI that meant I couldn't get it to work. This, and software upgrades are the only changes I've made in the last year and as I've now got a copy of the working files, after the next upgrade, if things do break, I can put them back.
I tried putting a chained cert in the CA cert and it didn't work, does the order of the certificates in the file matter? It may also be that the restart didn't work correctly or it needed a reboot after the change to make things work.
I'm not blaming pfSense here, I'm sure it was probably something I messed up in replacing the certificate. If I get chance I'll try again with a chained cert as the CA and update with the results.