By way of update:
Following Dave's excellent advice about how, if I would hire a solicitor once I was out of my depth then doing so now might stop me getting there, I contacted a solicitor (not a railway specialist but someone working in criminal law locally), we obtained copies of the evidence GA was relying on (ie the ticket and the RPI's record of my statement) and wrote back to explain what had happened. Meantime, GA told my solicitor on the phone or by email that what they were investigating was possible "altering" of the ticket, which is as expected.
After a month or so, GA have now written to say that they "normally prosecute all instances of fare evasion" but having considered my comments they are "prepared to close the file" on payment of the "outstanding" fare (which I actually paid when I bought the ticket but outstanding is how they describe it) and an administration charge. This comes to just over £100, of which I think £80 is probably the admin charge, payable within 14 days. I am in the process of paying this.
All things considered, this is a good outcome: quite expensive but that is mostly the legal fees and it was my choice to pay for professional advice, no prosecution, and stressful but over now. Thanks to everyone for their help. I can post more detail if it's helpful for future reference but I don't think I'd be adding much to other threads about carnets.
Speaking of which, I have since finished the set of tickets that started this off and gone over to buying individual ones. They're a good idea in principle but it's too easy for things to go wrong.