Hi,
I had a similar experience. I didn't have my I-94 (and it was expired) with me when I left the country last month for a vacation. My lawyer submited the original I-94 during the AOS application. I just made sure that I have my Advance Parole documents for re-entry. During re-entry, the IO stamped my AP with "Paroled until...."
Also, I called the BCIS hotline and explained to them my situation (leaving the country without I-94). They said I should be fine because I have my AP with me. Should you have any doubts, you can call BCIS and ask them for advise.
Good luck.
- Aelana