Had my first issue using the IID.

Diagnosed a faulty compressor on an RRS. Replaced with a new AMK unit. Worked fine, up and down no bother.
Re-flashed the RLM with the new software, as you do. Tried it out, had a red warning light on the dash, and suspension stopped working. Fault stored was B1A84 - Vehicle configuration data

Tried putting the new software on again, still the same. Tried to revert back to the original software, still the same...

Emailed GAP, explaining the situation. Received a reply 15 minutes later, with the issue having been identified as the software expecting the car to have the ARC system fitted.

A further 30 minutes later, GAP had provided the correct non-ARCM firmware, to allow the car to be programmed with the correct firmware. After which, no more issues

Had never come across this issue before, as it was the first RRS I had done with the IID. The rest have all been D3's.
In conversation with Patrick, he has said that in a near-future update, the correct firmware will be selected and installed, with no user intervention required.
He also made a point of saying that if anyone else has the same issue, to contact GAP, who will make the firmware available, if required before the update has been completed

So, 45 minutes in total from having an issue, identifying the problem, and releasing the correct firmware to rectify the issue. Can't ask for anything more

 2012 SDV6 - it's missing a couple of cylinders
2008 TDV8 - it was a labour of love and is much missed

Excellent response  2006 Supercharged