Upgraded to Logos 6 and lost all my highlighted NASB95 verses
Two things. First check the visual filter drop down in the resource and insure that notes (and note files associated with highlights in that resource are checked. Second, are you still indexing?
Even if they were accidentally deleted they should be recoverable on documents.com
And if that doesn't work, Tech Support can usually help you get them back from a backup of their servers.
And if even that doesn't work, get in touch with Dustin Masters -- he's one of the engineers behind the cloud sync platform, and he'll be able to do it for you. He's offered to help someone else in that regard.