Not sure if this will help as I am using quickbooks desktop contractors edition: 

however it worked for me. 

I was getting frustrated because I could not get the template I customized to be my default invoice template and what I found is that even though I can not delete some of the old templates but I can make them inactive so the other ones do not show up and it will make my custom template the only and default one that shows when I make invoices. 

Lists>Templates>Right click on the template you want to delete or make inactive>Click Delete template or Make template inactive 

Your welcome (: 

Signed - a fellow frustrated quickbooks user