I agree with René, the valve stem dust caps should have no bearing on air leaks whatsoever. It would be unwise to rely on such to seal a leaky valve even if it does work for a while. It's possible that LOTW disturbed the leaky valve by chance to stop the air escaping. Putting spittle on the valve stem with cap removed was the time honoured method of checking for valve leaks.

Tip: valve stem caps are available with an extended tool that unscrews the actual tyre valve within. A spare valve can then be screwed in to replace. May be worth having both, in the garage at least.

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