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I've been using MSpro for several months now. I have made annotations to many of my pdf charts. I am to the point now that I would like to modify the charts that have been annotated to make corrections permanent. 

Is there a way to list only the charts that have been annotated?
Otherwise, it will tak a lot of time to check each chart individually.
I have many charts and only about 10% are annotated.

Your not the first one who misses such a feature.
In the thread
I proposed adding filters for songs with notes and/or annotations.
Sciurius posted an SQL statement there that does such a selection.
Not as convenient as having a filter in MSP, but it works (I tried it).
May I suggest y'all use one of your unused searchable categories as a temporary 'annotations' field. It will cause work now identifying them now but should work as a workaround until something else comes along. You could also set up a coding system identifying permanent vs temp annotations.
If I would want to keep track of annotations in a separate location (which I do NOT want) I would create a collection like "Songs with annotations" for that purpose
I do know a tiny about sqls and databases, but don't really wish to go out of the app to do this manually.
I will likely just create a category or collection as you have suggested.

For the long term, the issue will hopefully be addressed eventually by Mike.

Cheers and thanks for the feedback,