Replying to myelf…
Project A was, as input dictated, 1080p 25fps.
Project B became, as it turns out, somehow, 1080p 50 fps (using the same kind of input, but possible that I have accidentally clicked frist video format entry whihc is 720p 50fps?! really hard to belive, but may happen.)
So, loading MLT with different FPS pretty much mess up everything, and really hard to figure out why.
Additionally it seems to be problematic (=impossible?) to change project FPS since cuts seem to be recorded in frames: setting FPS from 50 to 25 changes all cut positions to wrong places (probably twice the position). I can’t readily see any sane way to save a timeline in 50fps to a timeline in 25fps (to be able to MLT XML Clip load it into a 25fps timeline).
…not impossible, in fact, it’s funny: open XML, and change 3rd line frame_rate_num=“25” and that’s all, it is magically 25fps from then on and the cut positions, which are, contrary to my belief, in timestamps are proper too. And it loads as MLT XML, and does not mess up the timelines. Wheee!
But I guess it shouldn’t be that complex, fps setting seems to try change output format as well as cut times.
Another related problem seems to be that audio waveforms display have disappeared since MLT XML loading. Switching it off and on causes shotcut to read through all the files but nothing get displayed. (Video thumbnails work.) Since loaded MLT clip doesn’t have any properties displayed I can’t see whether audio was messed up, too [I guess it is].