Doesn't the capacitor get fitted to the battery end? In which case the polarity won't change so it should be just fine. Alternatively, you could get a non-polarised capacitor.
On the subject of power caps. What is the usual spec, capacitance and voltage? There is someone on Ebay selling them at around £4 for something that I could probably get from Maplin for well under £1, that's a tidy mark-up.
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