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Since 1040 and 1040-X are processed separately you should expect the refund shown on Form 1040.
That's why it is appearing on your 1040-X which will take several months to process.
I assume you meant to say "not allowing" rather than "now allowing"
this is one reason why an amended return should not be submitted until the original is fully processed - you get your refund. it is not possible to know if the IRS will process your amended return in time to prevent the refund as originally shown.
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