Re-Applying for EEA Family Permit Visa second time

Hello, my father in law arrived in uk in November 2015, by EEA familly visa for 6 months. Meanwhile he applied for residence. It was refused because of my mom employeer, he didn't answer to the phone when he was called for confirmation that she has a contract with him. My father applied again, a few days later after he recieved the rejection, 2 months ago. Today he recieved a letter from Sheffield Office that he have to leave uk because he didn't said the reason why he should stay in uk. But the letter it wasnt the same as the first one, with the reasons of rejection and details about. Just that he have to leave uk, and some advices about how to apply for residence. The rest of the letters are coming from Liverpool Office. So, we don't understand the reason why he should say the reason he wanna stay in uk since he applied twice for residence, and why the letters comes from different offices. If would be a real refusal, my mom documents should be send back, like they did the first time.

Please help, we dont know what to do or where to call! Thank you

Has he applied for a second residence card yet?

If he has, he can write to Sheffield, explaining the situation.

yes,he applied for second time before letter from sheffield to came,because first time was refused. thank you verry much.