More detail would be required to properly comment. But assuming you have a typical system - then no, formatting the Incoder hard drive should not effect the ClipStore databases on the XPression Output Engines.
But if if your INcoder has a 'Master ClipStore' installed on it, and is synchronizing to your XPression Output Engines, then its likely that formatting the INcoder drive could affect the ClipStore synchronization workflow you might have configured.