Please tell me there's an easy fix for this

is that my settings within a particular resource contain the option also to include multiple resources.

The panel you are showing is used to control which notes documents are enabled within a particular resource. If you turn one of these off then the notes / highlights stored in that document will no longer be shown in the resource you are reading.

The fact that both are visible indicate that you have created highlights / notes in both of these documents for this particular resource you are reading.

I've set my settings to 'most recent document'

This will cause highlights to be made in the most recent notes document - so, by default, using the same notes document for both resources.

To get round this you need to select the appropriate notes document once when switching resources.

Does this make sense / explain what you are seeing?

(That still doesn't explain why I could not deselect within the app...)

That is strange - and not what I see.

I've just tried it and the changes I make stay in place. Can you clarify exactly when they "unstick"?

So in order to accomplish what I desire to do (switch between a few resources and attach highlighted resources consistently), I need to manually select in settings the specific document rather than the 'most recent document'?

That would do it. Another option is to have "most recent document" and then when switching between resources explicitly specify which document you want to use the first time you highlight in a "just switched to" resource. To do this - don't use the "drag highlight" option (which you may be using by default) but double-tap on the section you are interested in, select "Highlight" from the popup menu and then at the bottom of the highlight menu there is an option to choose which document you want to use.