Hi @Neal Baker ,
Thanks for posting in the community.
For your problem, I have test on my side. When I logged into two OneDrive accounts on the same computer and selected the same folder location, the situation appeared as shown in the picture：
Is this what you mean by SP sites syncing in two top-level local folders at the same time?
If so, try changing the folder location of OneDrive for one of the accounts, keeping the folder location of the two accounts in different folders.
Here are the steps to change a folder location:
1, Open OneDrive settings (select the OneDrive cloud icon in your notification area, and then select the OneDrive Help and Settings icon then Settings.)
2, Stop all your sync and select a new folder location.
If you are experiencing a problem other than the one I described above, I hope you will send me a screenshot of the problem, which will help me better understand your problem and find a relevant solution. Note that where your privacy is involved, please code.
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