Just an idea I had, and figure I'll toss out in case it grabs the attention of GMs. Based on the movie Paycheck, where the protagonist makes a ton of money by reverse-engineering competitors' products... and on completion of the job, has his memory wiped back to just after accepting said job. After the protagonist's most recent job, though, the envelope of personal items contains very different things than he originally put in; each is a clue to lead him to undo or deal with whatever it was he did on that job.
This requires players accepting such a job. They're at the meet with the Johnson, then there's a discontinuity, same place but people are in different positions, an empty glass of wine before them. It has been a few days, and they're thousands of creds richer. The runners are sent on their merry way... and receive a package. If any members of the team opted out of the 'Run That Never Was, they could be the ones to bring the box-o-clues.
The runners have to deal with the results of what they did-- people and a corp or two reacting to the goals accomplished in the 'run.
None of the unknown actions are anything the runners wouldn't do. They just need to find out exactly what they did before their former targets catch up with them.