For your reference, my wife just used AP last month for travelling abroad and come back while continues to work on H-1B. I also got a couple of friends having the same situation for other companies, so, I think it is ok. But, be sure to consult your company's immigration/legal attorney first to get their "ok", because there is confusion in interpreting the AP rules. Technically, using AP will not invalidate H-1B, however, dependent upon the company's immigration representative.
Hope this helps.