Filing As Married Jointly vs Married Single

My wife and I are currently separated.  Last year we filed married jointly.  We sold our house late last year.  She normally handles the taxes, but hasn't submitted a return yet for us this year.   Earlier this year, she made a payment so we don't owe anything and she submitted an extension.   She recently told me that she needs to complete the taxes before the October deadline, and will take care of it, but I'm worried that nothing is done yet.  If I go ahead and file married single and then she files married jointly, can my married single be cancelled when she files married jointly?