I really ought to update everyone on the Trek Domane saga as I was quick enough to post something when I had the initial response from Thomas's Cycle Revolution.
After the chain stay broke I took the bike into Cycles UK in Chelmsford. They could not have been more helpful and were incredulous about the whole bottom bracket story. They arranged for the frame to be couriered back to Trek UK and put all the bits in a box for me.
When the frame arrived at Trek UK their initial response was to say that the chain stay breakage was my fault. On reflection, I think this is probably right after the hurried re-build and major fail that I had at the start of the H4C Perm
They hadn't been made aware of the bottom bracket issue at this point however.
I have to say that once they became aware of that issue, they could not have been more helpful. Everything has now been resolved to my complete satisfaction and I am feeling a little bad for doubting Trek in the first place
It seems that you have to fight to get past unresponsive dealers, or go to somewhere that knows what they are talking about like Cycles UK seem to do. If you can escalate the issue to Trek UK then I believe that they will deal with it fairly.