Hi there,
As someone who was affected by this too, having long lost the paperwork I had from Wagn, I did indeed change my ticket to go from a Hatfield > Hadley Wood and a Z1-6 Travelcard to a Hatfield to Z456 and a Z123 Travelcard (with both being zonal tickets, I didn't have the problem with a train stopping anywhere).
It did cost a little more but I wasn't going to risk a prosecution, although ironically it was the correct ticket combination that landed me with the threat of prosecution when it was deeemed that two tickets covering zones 1, 2, 3, 4, 5 and 6 didn't apply if split as there was a 'gap' between Zones 3 and 4! And for the benefit of the OP, that was incorrect and the claim quickly dropped.
Even if I had located the original letter (I carried a photocopy) that said it was acceptable to combine the two tickets I originally had, it was from Wagn which lost the franchise in April 2006. Although FCC didn't change things for some time, at some point (most likely during one of the many major staff changes) someone came along and just enforced the rules as is - perhaps having no knowledge of any easement.
FCC is fully entitled to do it, and nobody is left there that would know (the MD having left to East Coast and now off again to National Express, and when I emailed her she said she couldn't remember either way) so I think the only defence will be based around the fact that one ticket was valid at the point of being 'caught', or the fact you were sold the ticket combination every year AND never got in any bother during that time.
They'll have records of you buying the tickets if they were annual seasons, and they'll also know if you had any PFs. At the very least, they should consider letting you off as a goodwill gesture with you giving an assurance that you will either only use trains that stop at the splitting point or change your ticket to a valid combination.
I think writing to the MD might help here, as my email to head office saw my prosecution cancelled before the paperwork had even been handed in - so I never had to go through the ordeal of trying to argue my case (even though I was 100% in the right).
I wasn't even saving money by doing my split - in fact, it was the opposite. I split merely to get the use of Oyster in London. Going from Z1-6 to Z1-3 (and a paper ticket for the rest) was a pain because I occasionally touched out in Z4-6 and got charged, when I had a valid season in my wallet.
Was your Travelcard a paper ticket or on Oyster? If the latter, you could argue that you only use that combination for the convenience, because the industry hasn't extended Oyster to your originating station. However, if you did have Oyster and a separate paper ticket, then you presumably didn't buy them at the same time/place? That might impact on the argument that you were sold the tickets without being warned that you'd need to only use certain trains.