Glad to hear you like the update!
I use a text tagging system within the annotations themselves which are a combination of an identifier string and some status symbols. An example could be:
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SCI// Here is the content of my concern regarding scientific implausibility with the source text.
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SCI/- Here is the content of a note which is no longer relevant; I’ve fixed the problem in the text but wish to keep the marker for some reason.
Given the punctuation pattern, I can search for these either one-by-one using the Edit/Find/Find by Formatting... tool, or the main project search (and can then save them as Saved Search Collections for rapid use in the future). Since I mark something as “done” by changing the punctuation mark, a search for “SCI//” looking for all current science problems in the book will only find those notes which are still marked as not having been addressed.
This is something I’ve written about in the past, describing my methods in the hopes they will be of use to others:
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Tips for gathering markers into lists either as one-offs or automatically. Note the discussion here goes on at length, and I provide quite a lot of additional usage advice for making this system work fluidly.
Here is an older discussion that offers a less elegant technique using older mechanisms in the software.
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Method for tagging text and easily gathering all tagged text into a list.
And here is a listing of older discussions that have been had on this topic in the past, along with other solutions.