So the poor cogboys are up s¤"t creek in the Red Cages (along with the even poorer Psykers). Nice.

How would you handle dragonplate armour? It is like a set of power armour physically mounted onto the tech-priest. It can be removed, but probably not easily.

I fear that allowing him to have it will totally unbalance the sequence in the red cages

Dragonscale is not a bionic implant so it should be removeable. My magos militant sometimes (not often) took off his if only to perform maintenance upon himself. The party are likely to be out of comission for weeks if not months of warp travel, so there's plenty of time for Hayte hereteks to figure out how to remove the armour.

I agree, just nab them when the TP hasn't got the Dragon Scale on. What an awfully inconveient coincidence. Perhaps the Pilgrims specifically wait until he has it off, after all, TPs are known for their resistance to psykic powers.

OR don't even try to explain it, just make them unconsious and when they wake up TP doesn't have it on, just like the other PCs don't. As a GM you don't have to explain how it happened, no matter how indignant the player may get - that is aprt of the mystery after all.