Now there is another case with the same error message, only that the component is NATIVE and not imported.
Wishgranters suggestion of running a new alignment through the feature detecting step did not help.
Running a whole new alignment resulted in a slightly worse alignment - median and mean error 0.34/0.45, the old one 0.31/0.41 - which is around 10% !!
So what is happening here?
Is that because of deleted information in the cache, as I gleaned for Wishgranters answers?