First, are you backing up your Accordance folder before you sync anything? I compress my Accordance folder, date the compressed file (today's will be 150706), and drop it into one of those very small flash drives that can stay in the laptop. That way, if anything goes wrong, I don't lose anything. I'm also backing up using TimeMachine.
I had recently reinstalled Accordance because of another problem. The reinstall messed up all my syncing. I made sure that Accordance was running correctly and that Highlights and User Notes were up-to-date and backed up. Then I deleted all User Files off every other device but the up-to-date MacBook Air (MBA). I synced with DropBox then checked to make sure all the files were there. I think it took more than a single sync. I've got three User Notes Files, 16 User Tools, and 6 Highlights files. When I was sure it was all in DropBox, I synced with my other Mac (a mini) and with iOS devices.
Even now, I never sync without backing up the Accordance folder. There are 11½ years of notes and highlights and I don't want to lose them! If you're using TimeMachine and back up right before you sync, that will protect you, too. However, it's easier, I think, to just drag a copy of the compressed file from the flash drive to my desktop, unzip it, and recover just what I need just in case something has disappeared. And I don't lose the file on the flash drive when I drag the copy off it, so I remain backed up.
Now that it's all up and running, I'm not having any serious issues.
The User Tool I created to use as a prayer journal is kept up to date on the MBA. When I sync with my mini and iOS devices, User Notes and Highlight sync perfectly. There is always, however, a lag when it comes to my Prayer Journal (a User Tool). It is up to date on my MBA, but has no entries past June 28th on any of my other devices. Don't know what's going on there. That is a Tool that changes daily, just like my Notes and Highlights.
It would be helpful if you include what hardware & OS you're running in your signature. If you're on a PC, there may be issues specific to your platform of which I am unaware.
If you continue to have problems, do call tech support. The folks there are so very knowledgable and helpful.