No, if your return was accepted by the IRS, it will not later be rejected. If you would attempt to file a second return (which you are saying you did not do) the second return would be rejected for duplicate use of a social security number. It would not affect the return that was already accepted, it will not affect your refund method, it will not cause you to get a paper check, you just would not be able to push a second return through using any website.
It is best to use the IRS Where's My Refund tool to track your refund. Other systems update at different times, so if you go directly to the IRS site, there will be no confusion.
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