@schmuttis: The annot file is XML. It contains all the information in it to find the location in an epub for where an annotation should be. It would be possible to convert the locations in it the format that calibre uses. I have done it manually in the past just to check I was right, but, I haven't seen any automation to do it. The closest I have seen is a script to read the database on a Kobo device and add the annotations to calibre. That might be a starting point for anyone wanting to do this.
And for the record, I maintain the Annotations plugin. I occasionally say I will update that to save the annotations as calibre annotations. But, it hasn't risen to the top of my TODO list yet. It probably isn't going to be that hard, and adding annot file support would be relatively easy. But, that isn't going to help you at the moment.
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