请问file-I-539 时间的问题

My curent I-94 expired，renewing B status is pending. I filed another I-539 to change status to F1. Will they just deny my application just because I did not file the  I-539 in corect time? ( I thought my B renew can get aproved before they process my F1 appication). Should I send a letter to withdraw the F1 application or just make corrections to the F1 application after I get my B renew approved (e.g., submit new I-94 and correct I-20 sevis number)

Thanks!