You want to be extremely cautious when removing a question from your General Application, especially if it is being used as a qualification on any unarchived opportunities. Removal of a General Application question that is being used as a qualification could potentially result in removal of all related qualifications.

If the unarchived opportunity has an End Date (Public End Date for an automatch) that has not yet passed or has not yet been entered, the qualifications will be destroyed.

If the unarchived opportunity has an End Date (Public End Date for an automatch) that has passed, the qualification will remain on the opportunity as long as the Public End Date is not removed or changed until the opportunity is archived.
Note: It is recommended that changes to your General Application questions are made after going through Cycle Management (cloning and archiving of your system).