I am applying for a changeover with a different TOC.
That complicates things further, as the TOC you are now dealing with have no access to the season ticket records held by the TOC who issued the ticket.
Interesting. So it seems to me that head office are possibly asking for proof because they have seen 'DUPLICATE' in large, bold letters and have assumed that the ticket is a duplicate.
I will write to make them to make them aware that it is actually a replacement and highlight the fact that it is on the wrong stock.
I think this will be a good starting point, but you will need to be patient. It may help if you can ask them to contact you by phone so that you can clarify the situation verbally. Bear in mind that on the ticket they have two pieces of conflicting information and no way of establishing which of them is right/wrong.
I am concerned about the fact that my legitimate replacement has been issued on duplicate stock - and the implications for getting a changeover. Looking ahead, will there be proof on the TOCs system that it is in fact a replacement? Will the printed black writing in the bottom right corner make a difference?
This is an entirely legitimate concern. The TOC who issued the replacement ticket on the wrong ticket stock should have the ability to confirm what should have happened. The printed black writing in the bottom right corner would make that task somewhat easier, although if there records are as well organised as they were at the station I worked at it won't be a lot of help! A month's worth of paperwork chucked in a box file and rearranged every time someone wanted to look something up!
Do you have a copy of the ticket you submitted for changeover? If so, it may be helpful to contact the station who issued that ticket and ask them for a (certified/stamped) copy of the original ticket and the supporting paperwork so that you can provide them to the TOC processing the changeover. This, particularly the copy of your original surrendered ticket will confirm that your ticket was not a duplicate. I would hope that this would be acceptable to the TOC you are currently dealing with.
There is a lot appearing on this thread that will not be helpful to you, and I think that at present it will be most useful to concentrate on understanding the problem that the TOC is having and seeking to help them get to the right answer. I do not think that anything around where you live or work will achieve this at this stage as they are likely to be concentrating on whether or not they should be paying you the refund.
For the benefit of others reading this, I will point out that the issue of a duplicate season ticket always carries the risk that the original is still in circulation, and potentially in use. Where that duplicate goes to a different TOC to the one who issued it for some refund to be paid, the original ticket could also be still in use or working its way through the processes at the issuing TOC for a parallel refund. This isn't fantasy, it's something I have encountered more than once over the years.