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I'm not aware of a feature in any of the devices / apps that allows you to delete all annotations. I can say for certain the iOS app does not have this and you need to delete them one by one manually.
Annotations are one of the items that are synced, which is why when you delete and add the book in they are still there.
On an eReader I'd assume the data is in the database, and could possibly be edited, but I'm unsure wether those changes would be synced back up to the server, ie; removing the information during the sync. Thus editing the database would be ok until you next sync, then it downloads the info from the server.
For the ordering question, not sure how it's done on the eReaders, but on iOS if you delete an annotation then the rest do remain in the correct order, which is by chapter.
I hope that helps.
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