You do have to go through second inspection. There will be line of people, so they will write down your name. When your turn comes, one of the officers will call you and ask questions about your travel and the reason for traveling, your status, employment etc. He will take your fingerprints and stamp your passport and staple new I-94. This can take a little long than usual. For me, it was about 45 minutes wait.

I agree with Abhilasha_pokhara. For me the officer asked general travel questions and told I have to go inside the other room. At first got little bit surprised, so asked if all my documents are okay, and I told my AP expiring date has 6 more month. Then explained me that since AP means advance parole, they have to assign our entry I94 status as parole and they dont carry that stamp outside so you need to wait inside. Inside there were few people, about 4-5 waiting, many looked very serious. Waited for my name to call, around 15mins and same thing general questions, like how long u were there, what kind of work u do, and left. As long as your TPS and AP is valid you are good. Lets not call it secondary inspection its normal process. This was last year, few of my friends went this year for dashain and came back. good luck

Hi,

I came back to US on TPS advance parole in December 25, 2016. I had left my F-1 visa when I graduated and was only on TPS. I was taken to secondary inspection area (with 5-10 people on the line). The immigration official looked at my advanced parole document and asked me what I do in US. I said I work for an IT company. I had quit my job before going to Nepal. So, I told the official that I was offered another job that would start soon. The official then told me I was good to Go! I had to spend only 5-7 mins mins on the inspection area mostly to wait on the line.