My mistake, I used the D* word which immediately meant somebody was able to point out an error in the assumption I had made about the commode handles, thankfully I hadn't used the F** word!
It has worked out for the best though thanks to a chap called Adam - he questioned whether the handles would have been removed on both sides, or just one - simply because they had locked the doors on that side as the platforms were always on the other side of the coach. I went back through the reference material and could only find three photos of the platform face of the Thompson coaches. In two of them, it was impossible to say for certain whether there were any commode handles, but in the third it was beyond doubt.
I'm pleased the filler used was talc and paint - it came out quickly using a pin vice and 0.5mm drill, the handles were then inserted again with a touch of weathering to blend them back in.
Although it was a backward step, it was a pretty quick recovery and has also meant that its possible to identify which end of the coach would always have been facing the junction at Tiverton or the terminus at Hemyock. I can number each coach properly now, as well as form up representative trains. We'll call that a win.