Yes, Yuugo Tennouji (Mr. Braun) still has his secret job in the Beta world line after 1% divergence is obtained.
I base this on the wiki entry, which lists Steins; Gate 0 as its source. Here is what the Wiki says about this:
When 1% Divergence is obtained, Yuugo is seen running his shop, having apparently never worked for SERN in this world line. But as revealed by Steins;Gate 0, he still works for SERN in the Beta Worldline. Source: Wiki- Yuugo Tennouji
Edit: The anime adaptation of Zero is greenlit, but there is no broadcast date. I haven't read the Visual Novel.
Wiki page for Zero states,
The Steins;Gate 0 (シュタインズ・ゲート ゼロ Shutainzu Gēto Zero?) anime is an adaptation of a spin-off visual novel by the same name that is being marketed as a "true sequel" visual novel, as opposed to being a fan disc. However, though Zero is part of the main canon, it is narratively not taking place after the true ending of the original story but technically before said ending. Zero is a side story that explores events from the Beta Attractor Field's future that contribute in making the end of the original story possible.