OH MY GOD
YES
HOLY s#!+
I have nightmares that this is going to not get fixed in the next update and then us dozen micro/macrotonalists will have to wait another year or two to finally compose easily in alternative tunings.

I made a post about this on Reddit and also on Gearslutz:
http://www.reddit.com/r/Logic_Studio/comments/2o28g9/custom_tuning_is_broken_in_logic_1007/https://www.gearslutz.com/board/logic-pro-x/929522-logics-new-update-breaks-global-tuning.htmlThis is unbelievably frustrating.
It isn't only when unloading an instrument either.
I tried to work on some of my 5EDO/10EDO projects today, thinking "Hey, I'll just load all the EXS/Synths/effect plug-ins I'll need beforehand and sidestep the issue!", but then I found out that if you draw in a midi note anywhere, the audio engine resets to Equal Temperament. If you add a region, reset. If you delete any notes, reset. Sometimes just stopping and playing the session again after making some modulation changes would cause a tuning reset.
There is literally no work around other than having the tuning window open at all times and on another screen or monitor and constantly sweeping over to click on the radio button every time you perceive a global tuning reset.

Logic is the most amazing DAW for being the only one that gives you at least basic global historical/alternative scale settings. I really hope they haven't forgotten about us weirdos.