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To empty your queue, all you have to do is press the "Pause All Uploads" button which appears in the Status tab in SpiderOak. You can then de-select the file from the Backup tab. If the file has already appeared in your View tab, select it and press Remove. This may not appear to work immediately, because it can take the server several minutes to understand which data blocks have been removed before it will resume uploading the rest of the data.
If for any reason this does not work, you can always tell SpiderOak to empty the queue from the command line by doing the following:
c:\"Program Files"\SpiderOak\SpiderOak.exe --destroy-shelved-x
c:\"Program Files"\SpiderOak\SpiderOak.exe --repair
Please be sure to wait at least several minutes for these commands to begin running: they do not always generate text immediately. These commands will clear the queue on SpiderOak and allow you to select new files for your backup. It will also reset your Preferences, so please be sure to re-add any filter exclusions or size limitations.