Something similar: I just had an overheat problem with my iPad,and it turned off. Luckily I had onboard a backup one, so I was able to continue without problem turning it on..
Of course this generated two different logfiles entry (with few minutes of gap among them).
So, at home, I merged the two logs and obtained a good track (except for the few minutes gap, but that's not a problem).
The issue is that this flight track entry (obtained merging the two partial logs) is ignored by the new logbook selection of logs to be added to the logbook.
Is this caused by a bug somewhere or a behavior by design?
massimo