Clutches are still manual affairs--they use hydraulics and have a master cylinder and a slave cylinder. If either one goes bad, you can't shift using the clutch anymore. There's historically no "software" involved at all. If the clutch won't work it's a mechanical failure or fluid loss.
Fast forward to 2018:
If the "debug interface" (OBD type deal) on the car is in the mix, it means the clutch system is electronically monitored. Assuming this wasn't a scam, it is possible that the car monitors hydraulic pressure in the clutch system and a software issue was causing it to falsely report that the pressure was zero and so it disables the whole mechanism to prevent damage. That's pretty sophisticated, but entirely possible in a larger, newer vehicle. In order to fix the problem, they applied a software update and then everything was fine again.
Not sure you got scammed.
In my BMW, I had a bad O2 sensor that wasn't producing a code and it took the BMW mechanics four weeks to solve the issue of an intermittently bad sensor. They replaced a ridiculous number of components before calling in an Audi mechanic who actually had decent troubleshooting skills and found the $50 part that was actually at fault. I got to keep the new fuel pump, transmission, wiring harnesses, etc. Thanks BMW!