When you connect the car to IDS are you letting it find the car/PCM itself or are you trying to go into it on a 'no comms' routine, and adding the PCM number manually??

Usually (as you should know if a regular user of IDS) you shouldn't need to add any PCM numbers as it does them itself when it finds the PCM. It connects to the car then a screen comes up asking you to confirm what vehicle/engine it is.

Unfortunately it sounds like with you trying to connect/update it something has gone wrong (lost connection or whatever) and it has blanked the PCM. Usually going into it with no comms and adding the PCM cal number should get it back.

Wondering if it's a later IDS system running Windows 7 rather than the old XP and they've not supported the old cals from a nearly 10 yr old car?

They do daft thing like that sometimes, take things off for older models, which is a pain in the arse!

Not sure what to suggest.