i took my pumps apart regularly, on a rotation basis,and placed in a bucket-covered 'em with vinegar,and after putting them back together, ran them in vinegar for a minute or two, then rinsed 'em in freshwater-did a great job of removing the calcium/carbonate film off the cylindrical magnets!
i wouldn't worry too much about a miniscule amount of vinegar getting into your tank-it probly won't be able to impact on it much, given all the buffers present :wink:
i think that ReefLion's suggestion is usually the main reason for decrease in skimmer performance-crystallization of minerals in the venturi inlet.
the question is: by 'not working' do you mean less bubbles, or less foaming?-it could also be that you have less organics building up/unit of time, from better maintenance/water changes/more efficient feeding, etc.
also- if you're putting hands in the tank more often-this will interfere with the ability of the water to hold surface tension, which will = less foam.
hth