I did unlink then link account again (setting onedrive location to original local destination) and slowly but surely, the files on my desktop began to show back up to my onedrive online account.

Empty recycle bin then restart onedrive desktop application. Once this was done and I am satisfied that all files are present and accounted for, I go to onedrive online via web browser on pc and delete everything. All deleted files will then be replaced in their original location, new files remain untouched, copy time is minimalized. Windows will ask if I want to replace files with the same name, to which I reply NO. Once downloaded, exit onedrive and copy all files over to the original local onedrive location. My solution to this problem was to download all 250 gb stored online to an external drive by changing the onedrive location in onedrive settings. Then onedrive, trying to sync starts deleting my local files that match the ones stored online but does not replace the files it deleted. Since it took you over three weeks to come up with no solution, my local files grew, not syncing with onedrive online. It can upload or download this quite easily but synchronizing between two sources (cloud and local) it cannot do so well. In my case, this is approximately 250 gb. Onedrive is obviously not capable of an initial sync of large amounts of information. I hope you will share this with other people who are having my problem. This is not something that is on any Microsoft thread, but it should be. Okay, well you guys have obviously given up so I will provide you with a solution that I have found on my own. Hopefully it will help some of you with the same problem. Here is my correspondance with onedrive support.

I had nothing but problems with syncing onedrive files online and locally stored.

Onedrive sync settings windows 8.1