SpiderOak never removes content from your backup without you explicitly requesting it. If you delete something from your computer, SpiderOak will move its copy of the item to the Deleted Items bin display within that device in the Manage tab. Deleted items stay in the bin perpetually -- until you decide to intentionally remove them.
Many backup services only store deleted items for a short period of weeks or months, and if you do not realize the need to recover that file within this time frame, the backup file will be lost. SpiderOak prefers to take an all-inclusive approach.
If you wish to remove a file from your ONE upload you can do so by navigating to your Manage tab and selecting the device which houses the file you wish to remove. Find the file or folder within the file-tree and select it. You can then select the 'Remove' button to purge the file from your backup set. This will permanently and irrevocably purge the backed-up copy of the file from your uploaded data. You can only delete files in this manner from the device you are seated at. Files uploaded from other devices cannot be removed in this manner.