Here's what I would do:
- Plug the USB drive into the PC with the "master" library.
- open Calibre portable - sort the library by date (the date added column)
- make a note of the latest book and the date
- Use switch/create to switch to the master library by specifying the location on the PC
- sort by date, select all books newer than the portable library
- right-click and choose copy to library, choosing the calibre portable library
This assumes the PC copy is always the definitive copy. If you update the metadata on an existing book you could include it by always updating the date field. Or you could use a tag if you want the date field to always mean date added.
If you want to sync the other way - portable -> PC - then you need a way of identifying those changes. Again I'd probably use a tag.
The reason I'd would use this method is that it avoids manipulating files except through the calibre interface. Also, in most cases if you get into the habit of doing it regularly the changes will not be that large.
Oh and another tip - name the directories so that it's obvious what the libraries are ("usb_lib", "PC_lib", "my_lib", "wife_lib" etc)