@b4n's case should work, there seems to be a bug.
But generally, the current planning is to have a one-time migration if session.conf doesn't exist yet to cover upgrading from 1.38 to the next release (i.e. read all "session prefs" from geany.conf as if it were session.conf). After that, if session.conf already exists, no further migration is planned. I.e. if you track GIT master.