I'm not seeing the issue with a long running process. If the fake time is regularly synced to real time, it should not matter how long the process runs.

If passing data involves frequent switches between processes, then, yes, I see there would be a problem with syncing on every process switch. I think syncing at longer intervals would solve that problem. All processes could share the same fake time, but see the fake time skip a small fixed amount at fixed regular intervals. That fixed amount of fake time would take a variable amount of real time, which absorbs the small variations in real execution time.