OK, I tried it on another -current (32-bits) box and the two lines:
# update-mime-database /usr/share/mime
$ update-mime-database $HOME/.local/share/mime
(as normal user)
Brought my icons back
Just wonder why it did not work on this box (64-bits).
I'll try again later when I have some more time, but I'll consider the subject closed as this seems to be a very local problem on this particular box