The NY Times has an article out titled The Claim: Playing a Wind Instrument Causes Respiratory Infection.
“For years, scientists have noticed that people who play wind instruments seem to be at greater risk of chronic sore throats and airway inflammation. Some research suggested that saliva and microorganisms might build up in the mouthpieces, then get blown deeper into the instruments.
But until recently, scientists did not know whether the germs could breed and survive long enough to sicken someone playing the instrument a day or two later.”
Basically, yes, germs can survive a day or two and you might get yourself infected again. Bottom line is that you should clean your stuff out if you are getting sick or are sick…..and well, AT LEAST when you change a reed.