Ok after some time brooding about the failures (and interlude with kitchen renovation), two things for fixing the failed feeds:
- Prusaslicer has and option to raise extruder motor current during the filament change. I tried this and no more skipping. However, now the print failed because the extruder gear had grinded through the filament and I had to do a manual intervention, which kinda fixed the print but after that there were missed layers. So more extruder power is not the complete solution, but does help in some cases
- apparently the PTFE tube inside the extruder should be less than 2.0mm. Saw a post about this in Prusa FB group. While setting up the MMU2S, I didn't change the original PTFE tube thinking that the provided parts are the same as the one I already have. Maybe changing the tube would fix the feeding. The idea with the smaller ID is that it forms the tip bit smaller. I'll check the new PTFE tube if they really are smaller than 2mm