Since they pot pickups with wax (I think a mix of mostly paraffin wax & some less brittle wax like beeswax, I recall hearing), would you consider sealing it with a tiny drop or two of melted wax? They leave pickups sitting in it till all the air bubbles come out so it shouldn't harm anything.
Might make a bit of a mess, but it should stop dust or grit from getting into the pickup. I don't think that should create issues anyway, but if it helps you feel better to seal it, feel free.
If the covers look OK, and don't interfere with playing, I wouldn't bother switching them unless I was changing colour or going for wooden covers for example.