Dear cvoalex,
I managed to get some minor success today if I use the 0.1.2 version of the IDE (do not use the nightly build, keep it simple), install the new Arduino mbed-enabled boards version 1.3.0 (not the deprecated version) and update the bootloader by going to File -- > Examples -- >> (greyed out box??) --> PortentaH7_updateBootloader. Compile this and run.
This cleared up a lot of my problems. Maybe it might help you too.
EDIT: I should add that I still have to reselect the port every time I upload code to the board, but at least this uploads for me.