I ran into this with a user and thought it would be a relatively easy fix by telling Microsoft Excel to discard the changes. Unfortunately it took more than that, as the changes were cached for upload to OneDrive and discarding the changes from within Excel didn't remove the cached file. OneDrive doesn't control that file cache either. Instead, it's buried within another tool called the Microsoft Upload Center. The Microsoft KB articles I found referencing it say to simply search for it, then use it to delete the cached file. It doesn't quite work that way, or at least didn't for me with the Office 2016 applications. Searching gives you no results, making you wonder if you even have the application. It's there, but you have to go the long way through Windows Explorer.
If you're having the same or a similar problem, open the Microsoft Upload Center application. You can find it within your Office installation folder. This folder is typically
32-bit Office install - C:\Program Files (x86)\Microsoft Office\root\Office16
64-bit Office install - C:\Program Files\Microsoft Office\root\Office16
In that folder you'll find MSOUC.EXE, which is the Microsoft Upload Center application. Open that and it will show you any files that are pending upload to OneDrive. Assuming the changes you made are either no longer needed, or you have them saved already in a copy of the OneDrive document, removing problematic files from here will resolve the issue where you can't update or upload to OneDrive because of merge issues. Once removed from the Upload Center, the next time you open that document it'll pull down a new copy of the file to your OneDrive cache so you can once again work on it. That also means removing the file from the cache will also discard any changes you had made to the file since the last time it was able to sync to OneDrive, so keep that in mind.
If you keep having problems, within the Microsoft Upload Center settings, you can tell it to delete the entire cache and start over. That can be used as a secondary option if selectively removing specific files doesn't work. But again, be careful if you've made changes to these documents and want to keep those changes, as deleting the cache also means the changes you've made since the last successful OneDrive sync will be lost.
