well, Fred is fine, it seems the medicine they gave him has worked wonders and he is peeing fine, in the tray, back to normal running around attacking his sister. The next morning in fact, I was sitting in bed with 3 cats running about playing chase and hide, then Fred started playing bed mice!
The RSPCA got back to me, their vet is going to talk to my vet to try and clear things up, but so far haven't heard back from them. They did say though, that Ginger was thoroughly tested (a full blood panel) before rehoming, and it was thought that Gingers results would reflect Fred, as they are physically the same, same environment, siblings and so on, so at least we know that Ginger is just fine.
I think the vet was new, she was very young for a vet! so it could be she was trying to be thorough, which is not necessarily a bad thing, just made me quite panicked!
The RSPCA have asked that I transfer their care back to their vets now and they will cover the costs of any scans, if their vets feel Fred needs any, but I think they want to wait and do the blood test again when the cystitis is completely cleared up.
I was thinkning of getting some cystease to prevent any further flare ups, but Fred and Ginger regularly swap bowls, so would it be ok for Ginger to have it even though she has not had cystitis before?
Thanks for all the advice, I feel much calmer and if there is something wrong, then I am sure there is something that can be done to keep him healthy (prescription diet and so on) as he is happy and healthy in himself, is lively and bright and eating well.