Hello Hask,
If you're feeling brave and don't want to lose sync, you can add the missing thumbnails by hand, using the following method, for each book:
1/ With your favorite graphic tool, generate a thumbnail of the cover (8bit grayscale, 175 width).
As a Windows user, here is the command line that I use with irfanView:
Code:
i_view32.exe "C:\Calibre Library\Any Author\Any Title\cover.jpg" /resize_short=175 /resample /aspectratio /gray /convert="C:\Calibre Library\Any Author\Any Title\thumbnail.jpg"
2/ Get the calibre uuid for the book: right-click on a book -> "Show book details"
3/ Rename the previously generated thumbnail file using this pattern: thumbnail_{uuid}_EBOK_portrait.jpg
ex: thumbnail_a24d430e-944e-4712-a3be-edbf562b243e_EBOK_portrait.jpg
4/ Copy it to your Kindle, into /system/thumbnails
Et voilą...
Not the most elegant solution, but it works, and it can be easily automated if you have the necessary skills, or the right tools (I use Pentaho Kettle whenever I can...

)
Yack