On a deeper look it appeared that a few markups were still there, some randomly missing. We can kind of be sure that it is no human error – but we are stuck with any other kind of explanation. I just do not think that the import export is responsible, since I assume this must cause all data to be lost?
Anyways, it is a bit odd and not enough information for a proper support request. We put in the markups again now and will have to one-by-one recalculate sales prices/regular prices.