there's lots of PC synchronisation shareware available - i use synchromagic, - and since a reader is just a removeable drive as far as the PC is concerned you can easily set up your own procedures.
you can have 2 way synch , backup restore, one way synch (= make target match source) etc as you prefer.
with calibre for example I use synchromagic to maintain a backup library on another drive & also to backup my calibre metadata ( I do the latter for all apps that I use regularly e.g. vlc player, as redoing all user preferences after an update or a screw up is such a chore)
you'd need to test that altering device files via pc does not screw up any internal device indices., but I think that all the important stuff is in the .mbp files.
except maybe the master index used for searching. I have an untested theory that Kindle does not create the .mpb until you first open a book. & that that's how is knows which books to display as "new" on menu screen ( new = no .mbp ).
I've yet to research where the results of book indexing are stored in the Kindles., and thus whether there is any logic to using Kindle for PC as an indexer and transferring to Kindle after indexing has been done ?