You can haul them around if you like, might make for good company on those long drives lol. They're not necessary, probably kicked them up into the fender and got sucked into the intake cleaner box. As long as you're talking about the box the filter is housed in, you shouldn't have any problems, if you're taking about the intake box that's located in the intake tube between the filter and the throttle body, you may have some issues, but your filter should be preventing that, so I'm assuming you mean the air cleaner housing. Take the housing out, house it out and reinstall, it'll prevent them from contacting your filter and preventing airflow, though they sound like they're too dense to be sucked into the filter.
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