No, there won’t be any penalty, since you filed and paid your balance-due amended return prior to the extended filing deadline.
Generally, an amended return takes 6 weeks to process, but with the Coronavirus outbreak, it’s impossible to tell how long it would take.
According to the IRS's IRS urges taxpayers to use electronic options; outlines online assistance page, the IRS isn't currently processing mailed paper returns, and amended returns must be filed on paper and mailed.
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