Remember, the preferences folder is now being
shared (by a multiple you

)
All sorts of confusion on who's
version of the current settings is really
current happens with 2 sessions because Sigil write the current
state only when it closes a session
Simple example of a
lost state
edit a book
Do multiple (progress) saves
manage to crash Sigil

or close it before the other open session closes.
The last used file list knows nothing about a file that has multiple saves done.
I don't know the solution on how to manage (refresh) the states saves so I avoid when possible by using Notepad++ for my reference clips.
1 possibility is to force Sigil into a Read Only mode if it detects that there is already an active (write) Sigil instance (the read only Sigil will not block a new Write Sigil if none exists)