That is an extremely rare issue, and was likely caused by unplugging the ECU.Don't know if this will help, but here's what happened to my 2000 with 1.8T ATW engine. Car was fine before battery went dead after sitting a long time. Had to jump start it.
After that, car would start one time only. After shutting it off, it would crank but not start again unless I either disconnected battery or unplugged ECU for a few minutes. Then, it would start again once but not a second time.
I had to replace the ECU. Got a used one and made sure it matched the part number of the one coming out. It was plug and play and the problem never came back.
You should never disconnect the ECU while the battery is connected.