I539- Notice to intent to Deny

My Employer filled H1 and H4 extension together, When my spouse was in INDIA.
But today I got letter of I539- Notice to intent to Deny saying she was in INDIA during filling .we were not aware that we can not file extension if we are out of country. Last week she already got H4 visa based on my I797. Can she come on VISA now?
Do we need to reply of the letter? Also will deny effect future extension or visa?

Please suggest

Its because she got vusa stamping done that is why USCIS denied the extension of status. She is good to enter on H4 visa and once she is back you can respond to RFE with the copy of I-94 issued by the CBP. USCIS will anyways deny the extension of status.