You reported your income twice: once on  F1065 and again on F1040 Schedule C  and you ask if you should Just Not Worry About It ??        Sure - don't worry about it.

Edit:  I missed the 'extension' in the question.  So only reported income once?   However, you can't ignore filing a 1065 return if IRS is expecting one.   CP575A letter indicates what type of return IRS expects to be filed for the EIN issued.