Thanks @LorenHawthorne for highlighting the danger of this auto-save “feature”. You’re the 3rd person (including myself) that I am aware of that has hit this landmine. We’ll go away and think about how not to trip up users in future. There’s a fine balance between pestering users with a “Do you want to save?” message every time they hit print and autosaving (on the assumption that what is in that window is what they want to be saved). Hopefully there’s a happy compromise somewhere – probably when they change books, to ask about saving the current contents before switching, and then making sure we refresh the contents to the new book right away.
BTW - one of my tips is to regularly create an Archive (.zip) file which contains all these settings files. So if something does get accidentally overwritten, or deleted, it is easy to open the .zip file and retrieve an earlier version.