Those few hundred duplicated rows turned out to be a HUGE problem, the automatic compaction started throwing errors that "Keys must be written in ascending order.", and successive failing compactions started to fill the disk until it ran out of diskspace which was a bit sad.
Right now we're trying to figure out how to remove the rows that get corrupted by upgrading, hopefully it can be solved.
The way we solved this problem is that it turned out we had only a few hundred rows with unicode keys, so we simply extracted them, upgraded to 0.7, and wrote them back. However, this means that among the rows, there are a few hundred weird duplicate rows with identical keys.
Is this going to be a problem in the future? Is there a chance that the good duplicate is cleaned out in favour of the bad duplicate so that we suddnely lose those rows again?