Sorry to add to an old thread, but I see this one ends unanswered.
I've sync hundreds of my calibre ebooks with my Kindle (1 device, 4 android, 1 iPad) and I use a slightly different route.
I know calibre has a device sync option, but honestly I never used it. I use the "my own document archive" capability of kindle to read documents I generated and store it in the cloud. Then each of the kindle I have (for the family) can download just the books they want to read.
Each kindle device and android/iPad app has an email address randomly generated that looks like:
kindle_xxxx@kindle.com. You can see this in the setting of each kindle device/app, and you can see it if you browse to amazon.com
Click:
- Your Account (a menu tab near the upper right side)
- Manage Your Kindle (from the drop down menu)
This will open a page showing all your documents (not just one purchased from kindle).
Click:
- Manage your Devices (from the navigation menu on the left)
This will list all your kindle devices and the email address associated with each. (Note that you can change your kindle email address, see the instruction there)
Now any .mobi (actually also .pdf) file sent to ANY ONE of this email address ends up in your personal document archive, AND is ALSO whisper-sync to the one specific device that email is associated with.
So, get calibre to generate .mobi files (fixing any meta data first, if you can, it keeps your library/document archive clean) and email those to your kindle.
Incidentally. any of your other kindle devices/app can find these documents by choosing to browse "all Items" or "in the Cloud" (different app refers to them differently).
Done, and I hope this helps.