You should first be going to the attorney who filed the case on behalf of your company for advice on this.
While your trip won't invalidate the Approval of this extension petition with a new H-1B validity period, it will invalidate the portion that is an extension of the current stay in the U.S. - even if approved that way (with a new I-94 at the bottom). You can leave and return before the expiration date of the current H-1B using your current H-1B stamp, but on the day after the current H-1B expires you will NOT be in valid H-1B status anymore, even if you have a new H-1B Approval Notice saying that you are.
Your company can withdraw the currently pending extension and file for a new extension after your return from this trip.
Or, you can leave close to the expiration in September, apply for a new H-1B stamp using the new Approval (as your current H-1B stamp will likely be expiring then as well), and return to the U.S. using the new stamp and Approval Notice. You will then once again be in valid status under the new H-1B extension.
Nothing about the pending extension will prevent you from departing to travel to India.