I could see having slightly different covers for paper and digital but only because of resolutions, like Lin said. You want to build up brand recognition and having different covers on different sites could be very confusing for readers. That being said, I doubt too many readers buy from different stores. I certainly frequent the same one unless I need to use a different one for a specific reason.
I'd say keep them the same! You can always try switching them all later if you're experimenting on covers. Or start a post here to get them critiqued if you're worried about effectiveness.
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