Maybe you could put down a paper plate in the enclosure before you're to offer the feeder to help against eating substrate (though some of mine whip around and drag their feeder all over the place so that's not fool proof) or a couple days/day before you're to feed put down paper towels or newspaper instead of your loose substrate then the day after feeding you can go back to the loose stuff (downside: more work and waste of bedding). I wouldn't worry about them eating some substrate though and just feed in their enclosure.
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