Expanded project tree in Project Tool Window collapsing automatically if I'm returning from hide mode after 'some' time (it keeps expand tree if I'm returning to Project Tool Window after 'short' time).
How to disallow collapsing project strucure from Project Tool Window after returning from hide mode?
Please update (or just try .. if your license is not covering it) to the latest stable 2016.3 version.
Accordingly to this IDEA-152049 ticket it should be fixed there (I do not use this panel in such mode so was never affected .. but accordingly to the comments of users who faced it .. it works OK for them in 2016.3).
If it's still not fixed for you -- have a look at related tickets that are still not closed -- maybe you have slightly different scenario.