For what it's worth, it looks like you can sync the reading position only (no notes or highlights) between sideloaded non-Amazon books between Kindles and Kindle for devices using the ASIN metadata trick.
See this thread here for someone who describes how she
sideloads her books onto her iPhone and other people's comments regarding changes because of firmware updates.
Here's the really long thread in which
the trick was originally discovered.
Here's a thread with a
utility to help automate the process.
And here's the
MR wiki page on it which collects most of the useful info.
Hope this helps.