Ohh, I found some old posts from november (maeof vs. tiger):
-"Example player A was in an alliance with Construction officer position 25 days.
Leader made player B Construction Officer and player A became simple member.
Player's A loyalty status will come back to 0 days?"
-"Loyalty status depends only on how long is someone in alliance, not on how long he was on some position."
Then again manual says that change in position resets the timer.
Oooops, too bad for my OLD science officer...