B1/B2 visa while H1B visa process on

My H1B case got selected in the recent draw for 2017. Mean time I need to visit US for official purpose for a month before September 2016. Since my B1B2 visa got expired, I need to apply for the visa again.

My question is if I apply B1/B2 visa while my H1B are in progress, will affect adversely to my H1B petition?

That is ok. You can appear for B-1/2 visa stamping while your H-1 petition is under process.