Yes, in fact it was so far away from the original topic, I’ve split it to a new one.
What might be going on here is that you were messing with the checkboxes on Windows/Mac, but never really noticed, because you also changed the setting to always compile everything no matter (a setting which doesn’t exist on iOS).
These checkboxes are meant more for things that never change whether you would want to include them, like chapter notes or old revisions. If something is included, it is part of the work, if it is excluded it is not. The notion of changing that designation frequently or en masse as thus very strange. That is in part why it is, as you describe, laborious and convoluted. There is no reason to optimise a tool like that, for what you’re doing with it (inadvertently or no).[1]
Here are some tips for more effective selective syncing.
That said, there are conveniences on the desktop. Refer to §23.4.1, in the user manual PDF on the Contents tab, under subheading Content Item List, which concludes with tips on bulk changes to the values shown here. ↩︎