I did a bit of poking around and it looks like OS X had (and still has) a background-process which will clear the temporary files after 3 days of non-use. So it is quite likely that if you were to re-run it, it would still take about 3 days and q2cli's temporary log would be cleaned up by your operating system.
This has the potential to explain a lot of weird things we've seen in OS X. Thank you so much for bringing this possibility to our attention! We'll try and figure out some work-arounds.
Until then, I don't really have a good suggestion for how to fix this in the short-term. Sorry 