should not be a problem
I too am leaving country shortly and in a similar situation as u (expired visa stamp, but valid H1). Spoke to my attorney and she did not foresee any problems, just that she sent me copies of my 485/765/131 receipts to carry with me. For all practical purposes, I am told, AP is a multiple entry document, that u can photocopy and use as often as u please (until its validity).
As a sidenote, you will be sent in to talk to a second immigration officer on your return - not an issue, just standard procedure. Be sure to carry an emp Verification letter too.
Hope this helps.