Exactly my problem too. I unplugged a remote HDD too soon before LR had closed out properly and when I restarted LR it squawked about having to delete all my synced data and try again etc. I went through the pain of deleting my synced data on the cloud and saw the whole lot get wiped away, but having logged in and out more times than I care to remember, despite having just 4 files in the sync collection LR tells me I still have 878 files to sync and not to shut down otherwise I have to sign in again to restart the syncing. Cannot find an answer to this problem and getting pretty fed up trying to find out why it won't reset its counter properly. HELP anyone?
OK, so I went right back through everything again. This time I loaded a spare LR catalogue file, opened it, closed it, shut LR, restarted LR, loaded the main primary catalogue again, made sure I had a web page open and was signed in to my Adobe account and then went back through the delete all data rigmarole again. This time it WORKED and I have now got just two files in my sync collection and only two files being shown as syncing and only TWO files on the cloud side too. Not quite sure why it worked out this way, but just happy to say it did. Good luck with your mis-matched photo count problem.