In general I always delete a book from the reader after I have finished reading it. I then update the tags in calibre.
I currently have 2 specific tags I use for Calibre Sorting - Read and Copied. I can then filter this down so that I have a list of books that have neither tag - I can then determine what needs to be copied across to my reader.
There are other tags I use but these are for different collections etc.
I have found that this works rather well and keeps my reader up to date with books I want to read without having to search through stuff I don't want to read...