You can turn off auto-sync/whisper-sync on each device. Just follow these steps,
Syncing Material Across Your Devices
If you read the same Kindle Store book across multiple Kindles, you'll find Whispersync makes it easy for you to switch back and forth. Whispersync synchronizes the bookmarks and furthest page read among devices registered to the same account. Whispersync is on by default to ensure a seamless reading experience for a book read across multiple Kindles.
To turn Whispersync off:
Visit the Manage Your Kindle page.
Scroll down to "Manage synchronization between devices. Learn more." and select "Learn more."
Select "Turn Synchronization off."
Once you turn synchronization off, your books will still open to the last page read on that device, but Whispersync will no longer sync bookmarks or the furthest page read with other devices. If you would like to sync the book manually, press the Menu button and select "Sync to Furthest Page Read."
Found this on Amazons site
. However, I'm not sure what kind of affect downloading new books will have on your current bookmarks. Good luck
.