Is this sentence correct?
Since we have not received a response from you, we assume you do not want us to take further action and therefore we will close this file.
Seems okay to me, as long as something else in the letter let the reader know what the situation is.
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.