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1) I dont recall not deleting them was intentional or not, but given how annotations are stored, it's not likely to change. Annotations are actually stored in three places, the database, the config folder and inside epub files (unless you disable the latter in the viewer prefs)
2) As long as you save and re-import epub it should work assuming again you haven't disabled saving annotations in file. And if you are using annotations in both the local viewer and content server, you will need to enable the viewer to view annotations form either a specific or all users in the viewer preferences.
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