Jag I'm not sure how I missed all 16 pages of this thread, but there goes my afternoon, lol :P

That is impressive, it puts my fish house to shame, so neat and tidy! Credit to you those tanks! I hope to have something similar when we have our own house, It's just not feasible at the moment in rented accommodation.

It does sound like the plants were a contributing factor. When plant matter breaks down this produces ammonia, adding to the bioload in your pond. The oxygen exchange is also stifled when the surface is covered with plants, plus as previously mentioned oxygen will be removed over night. I'd say this change in water chemistry and the fact you had no filtration running which (with a decent population of aerobic bacteria) would have coped with the increase in bioload from the plant matter. To a certain extent the mud would have acted as a natural filter but it's a poor filter in an artificial pond with a larger concentration of fish than you would get in the wild, this is why people tend to use an artificial filter. I can only really echo what has previously been said about the long term build up over the course of the year, coupled with this change in the nitrogen cycle has caused loss of oxygen and/or an increase in ammonia.

I'm afraid it's a mixed bag - some bad news, some good:

The hole now looks bigger (wider) on both sides. It's quite shocking to be honest, however it isn't as raw (pink) as it was and the swelling around the middle of the fish has gone.

Behavior has also improved with the fish hiding and reacting better. Previously if I moved a rock there was no sense of urgency to get out of the way which made catching very easy. Tonight I moved a rock and the fish shot out and under another rock.

I also fed a spirulina tab to gauge interest in food and response was very good, I just need to take care not to overfeed. I think I'm going to continue with the Octozin anti-parasite meds and keep fingers crossed.

I have a question then. I'm fairly sure that the fish has a parasite. Should I dose the main display tank with meds too?

Thanks for that, really appreciate it! Unfortunately Metronidazole is very difficult to get hold of. The only way I could get it is through a vet, and I'd have to get a consultation first. I work 7 days on/7days off and I won't be off work now until next Thursday. By then if the treatment hasn't worked the infection will be much further on and treatment is expensive (£80 for metronidazole, plus the vet's fees). Octozin is the closest I can get (I think it's di-metronidazole and salt basically anyway).

Thanks, I'm going to do a couple of water changes over the weekend and start dosing anti-bacterial meds next week and bring the temperature back up to around 23C.

Update:

I've dosed octozin for 2 days (third and final day today) and hopefully this will kill any parasites that may have caused this wound. I've also dropped the quarantine tank temperature to 20C to slow down the bacteria in the wound. Will let you know how it goes...

Found 6 boxes of Octozin in the garage last night!? So I'm goign to try that, apparently it's commonly used for hole-in-the head and other parasites so it might work... if it is a parasite that is.

It looks very swollen at the back end of it's stomach also so I think whatever it is has turned bacterial. I've transferred to a quarantine tank, but prepared for the worst to be honest...

I have set up the quarantine tank and have some melafix, I'll keep you updated. I have some other treatments in the garage (I think I have some metronidozole) so will dig them out and see what I can find. I am wondering if it's hole in the head disease, as holes can form along the lateral line too. I'm sure this is a disease or infection of some sort and not an injury, I can't see how it could have got an injury that punctures all the way through, unless I have done it inadvertently when moving rocks around, but it's unlikely I would think.

To be honest I think there's only one way this can go. The hole is about 4mm across and the same on both sides. Here's a picture, sorry it's not great but petricola never stay still!