Firstly, if you delete a collection on the device, it does not delete the books that are in the collection. So, you don't have to empty them first.
If calibre and the driver configured correctly, it will do all the collection maintenance when you connect to calibre. It can do this for all books on the device that are also in the calibre library. Have a look at
Quick Guide to Shelf Management with calibre for instructions and lots of discussion.