We have a customer with an old bpt entry system, which connects to an analogue trunk on the phone system via a bpt IT/200 box. The bpt system also includes fob entry for staff. The customer is due to be going to a cloud based IP system and the only analogue interface is an ATA. Does anyone know if a trunk based entry system would function if connected via an ATA?

That's a question for the UcaaS provider.

Since an analog telephone adapter provides dial tone, I would expect it to interface with the trunk port of a BPT IT/200 just fine. This is provided that the ATA provides enough voltage to trigger said trunk port. I've had luck with the Cisco SPA and 19x series adapters.