What should my friend do if his eVisa application is flagged and he has to attend an interview?

He may not get access next time

Wait for what? If the embassy is asking for an interview, the agent can't do anything to change that. The applicant has to go to the embassy for the interview or have their application denied.

Different countries different regulations ...where did He apply for His evisa and which nationality He has? Did He apply in His Home country?

Which e visa ??

Why would he need to fly? He should already be in the country where he applied. Sounds like he didn’t follow the policy and the agent is telling him not to continue because they will see in his passport that he wasn’t there when he applied.

No matter how talented the "agent" may be, the actual Thai E–Visa applicant should login onto the Thai eVisa website and find out exactly when the Thai Embassy/Thai Consulate scheduled the interview and go to the scheduled interview

if the Thai E–Visa applicant used an agent because they don't have the minimum proof of funds (money) and the agent "fronted" the money, well, highly doubt any Embassy/Consulate of any country would allow an "agent" to go to any visa interview in place of the actual Thai E–Visa applicant:

sure wouldn't work for their own country's Embassy/Consulate, why would it work for any Thai Embassy/Consulate??

In Thailand anything is possible. Only Buddha knows. TiT.

If he doesn't attend the interview he's not going to get the visa

Hopefully he was in that country when the application was sent and is still there. They will go through his passport to check

He goes at the time and place the Embassy requests