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Can I stop syncing a folder by just deleting it in my file system?
Yes. However, it’s important to be certain that you’re deleting the synced folder, and not just a folder inside the synced folder. When you delete a folder inside a synced folder, this change is sent to SharePoint. This means that if you have Delete permission, the folder (and items in the folder) will be deleted. To make sure you’re deleting the right folder, use the Stop syncing a folder... command as described above.
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