To see exactly what is occurring here, can you please check your Events page here and let me know if you see the deletion event mentioned in the email that you received?
It’s possible that if you’ve renamed or moved some large folders that this may be the reason for the email that you received as Dropbox can see these actions as a deletion from one location and addition to another. When you check the Events page, it will be a good way to see clearly if you have a deletion/addition event that could explain this. In any case that files may have been deleted, we will be able to assist with restoring them from our end.
In terms of your syncing issue, I’d suggest restarting the device to refresh the app if you haven’t already.
Finally, in regards to if you have any Symlinks on your computer, you can run a simple command on your computer to locate any symlinks within your Dropbox folder. The exact steps to do so are in our Help Center article here under point 7, the steps are dependent on your OS.
Let me know what you find - Thanks!
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