Support for cleaning up imported PDF score

I recently tried the "read PDF" service on a score. The result looks very promising and would save me a lot of work keying in parts of the score (for personal use certainly). The "notation" looks quite good, but the service missed a lot of the n-toles, i.e. we have quite a lot of irregular bars as the notes do not sum up correctly.

I assumed, there is something like "mark these notes and make an n-tuple of it" what would get the timing right again.

I hope I may post three lines of the score here without going to jail.

original score:

converted result:

There are some missing rests and beat changes too, but these are easy to insert. It's mostly the n-toles that I cannot create from existing notes. I just can delete them and re enter them manually. Can that be? That would result in deleting most of the already "good" score.

I had worked with Sibelius for quite a while where I also can OCR a PDF to a score - which is of similar quality. But there I just mark the notes, type ctrl-6 and voila, the wrong part is a 6-tole again, the "bad" bar sums up to a nice 4/4.

Did I miss something? Is there any add-on that does this? Am I out of luck? Nobody else had this kind of problem before?