I think I found the answer to my own and lertr's question!!
I'll write here before I forget after like 10 hours of attempts (yes... I know...)
0) load your mobi into calibre and make sure you are happy with all the metadata (title, author, cover, etc) as you cannot change anything of the file at all after you wise-process it.
1) take the file from the calibre library folder, copy it somewhere else (say your desktop) and process it with wisecreator / wisecreator.exe
2) remove the old mobi from calibre deleting it via calibre interface itself (just select and hit delete, to be clear
)
2) add the new mobi from desktop\title*wordwised folder to calibre library via calibre > add
NOTE: from here on, the file cannot be edited: the md5 of the calibre library must not change or you will loose either the cover or wordwise (can't recall which)
3) send to kindle: use calibre > send to main memory
OPTIONAL: use MOBIeditor v1.1.exe to verify that the process didn't mess with the asin code in the metadata (i.e.: the asin of the mobi on your kindle is the same as the asin on your WordWised folder. If you did everything fine, this should be unnecessary
5) add the .kll file ( from the sdr subfolder of your WordWised mobi - to your Kindle\documents\author\book\book*.sdr folder)
IMPORTANT: do Never move them again... whatever you do, don't rename or move anything in those kindle folders... even if you move them back, they will loose their cover and you will have to repeat everything from scratch
--- I tried this with 6 books and they are all hits, the process works for me: kindl paperwhite 4, windows 10, calibre 3.34