That dialog is built into Apple's Cocoa frameworks which BookMacster and most all apps are built on nowadays, and it is not one of my favorites.  Usually I have about 30 apps running on my little Mac Mini, and although I try to be fairly religious about hitting ⌘S before switching windows, inevitably either I forget a few, or I accidentally hit a key and changed a document in some app.  So, then when I go to shut down, usually once every couple weeks, I get a few of these stupid dialogs popping up, and I sit there and scratch my head and wonder "Now did I make a change that I want to keep in this document, or was this an accidental key strike??"

With many apps, I can find out by looking in the Edit menu at the Undo item.  Whatever I did should be stated there, although it often doesn't tell you much.  Example "Undo Typing".  Duh.  For more info, I can hit the Undo and see what happens.  If it was something I want to keep, then I hit Redo and Save.  It's not a very pleasant experience, but it's acceptable.  Tip: You may need to click Undo more than once.  When you've undone back to the point of the last document save, the so-called dirty dot, the black dot in the red close window in the title bar, will disappear.

Now, that being said, F451 and his spouse have a good point here because in BookMacster, you can change both bookmarks content and settings, and these are in different tab/views, and since we have not yet programmed all the Undo actions, many times the Undo menu item will simply say "Undo".  Then when you click it, something happens in a view that is not currently being displayed, so you have no idea what you did.

So, it's another issue entered into our bug tracker.