I had this problem with a ticket of this route restriction for most of the year. Here is my story of unfortunate events:
I am a student and always have bought with my railcard the £18.35 Southampton Central to Walmer via Barnham open return whenever I go home. Before that I bought the same ticket from Portsmouth until I moved university. I had a summer job at PC World which involved travelling back and fourth each week from home. For ages I used to travel the route through Ashford and Brighton, or sometimes Tonbridge and Redhill without trouble. South Eastern allowed everyone on the high speed trains without a supplement until they fixed the sea wall between Dover and Folkestone so for a while I travelled via Barnham from Victoria before going back to my usual route after the wall was fixed.
Then the problems with Southern began, I bought the +ANY PERMITTED ticket as a one off for £49 as I kept being late to work, but realised I would barely be earning anything if I carried on. I tried split ticketing and using advance fares but did not save much. When I called Southern to ask them explain, they told me to carry on buying the via Barnham ticket and to just use a South West Train instead and to explain my case to the conductor if questioned which I did for the whole summer - most of them never battered an eye lid.
It has got to the point now that Southern trains are so unreliable all the time that I cannot make any travel plans without the worry or stress that they might be being delayed or cancelled at a moments notice. I don't mind travelling with them instead of South West Trains to arrive home an hour or two later to save £30.36, but knowing that I might not even get home at all is ridiculous. I have many times been so delayed arriving at Ashford that I have nearly missed the last train and nearly been stranded.
These days if I am travelling early enough in the day and not in a rush, if is a Southern train, I will use it. However if there are delays, cancellations or no trains at all then I get on any one of the many punctual South West Trains to Waterloo and state my case to the conductor each time. Most of them are understanding although one a while ago shouted at me about pulling the wool over their eyes lol. Still never charged me a supplement though. The ticket always works the gates at Waterloo and Waterloo East.
After getting to Waterloo I then pay for underground which is cheap enough with contactless to St Pancras and get on a high speed train home. Lots of people on this forum have disputed their validity although it doesn't say on the ticket it is not valid. Also if you put in a time very early in the morning into a route planner it will give you an itinerary to travel from Brighton to St Pancras on a Thameslink train. The ticket never works the gates but no southeastern conductors have ever questioned me nor have any gateline staff denied me through.
The bottom line is I would not worry too much and to take a reasonable alternative route if you need to. Be honest and politely explain yourself how it is not your fault if you are ever questioned or told off. The ticket may not be valid but the conditions of carriage still contractually bound them to get us from A to B even if it means by came as a last resort. Plus I don't know about you but I certainly can't afford to pay more nor should I be forced to pay twice as much for a ticket to travel to the same place just because Southern can't get their act together!
