I keep a separate racking hose and bungs for sour beers, but everything else (even the autosiphon) I use for both with no problems. I clean everything with hot PBW, rinse well with HOT water, hit it with StarSan, and let everything drip dry completely before re-sanitizing and using for non-sour beers. No problems.
BTW I see you are in Austin. I'm brewing a Flanders Red on Saturday. If you want to come by and drink my Berliner Weiss drop me a PM.