I am an American, and most of the other folks on the project were as well. I did go through an interview with Customs officers when I returned to the US, but it didn't affect my ability to use GlobalEntry. I don't have clearance, but it might cause questions if I did apply for that in the future.

I've also been to Syria as a tourist several times, and at one point had to maintain a second passport for visiting Israel or the West Bank. You can't travel to most of the Arab world if you have Israeli stamps, but you can get another book from the US to keep them separate.

Sorry for your friend. Borders are bullshit.

Second passport is fine, but they stopped stamping at Tel Aviv many years ago. I still got a stamp last time I went to gaza, but that was about a decade ago and pre current passport. Obviously not a concern now)