Any tuners in here? Autotuner question

[GVK]

Took car (VW Scirocco 2.0 TDI) over to Newark today to get swirl flaps mapped out, keep getting faults and EML on with them, and the proper fix is a new inlet manifold at about £700 - nope! Sadly after about 20 mins of car being in workshop he came in and said can't communicate with car with his AutoTuner flash tool , normal scan tool will communicate and check codes (I've never had issues with scan tools and I have a few) as he had other customers and appointments this afternoon he couldn't continue. Advised checking the OBD port for backed out pins which I've done now back home. Can't see any issues with the port. So a bit stuck.