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Correct - if you move a file out of a folder that is being synchronized, then that file will be removed from all the folders in that sync. If you move the file to another location that is part of your SpiderOak backup selection, this file will continue to be backed up normally. If you move the file to a location which is not selected for backup, SpiderOak will move the file into the Deleted Items bin under the associated device on the View tab. This will also occur on any other computers which are included in the sync.
To remove a file without having it affecting other folders included in a sync, you can delete the sync before committing these actions. You can also edit the sync so that the computer where the file is being moved is no longer part of the sync.