When you have more targets using the same VI's in the project, the bookmark manager is searching through the VI's one time per target. Therefore when you have 4 targets, it searches through the VI's 4 times and show the bookmarks 4 times in the bookmark manager. Furthermore it takes long time to search through the files 4 times.
Se here how my bookmarks looks today.
I have changed my own bookmark manager, so it can filter from which targets the bookmarks should be read. It is easyer to overview, and it is much faster to populate the bookmark list.
I will suggest it will be implemented in the official version.
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