Her H-1 will consist of two parts - I-129 processing and COS from H-4 to H-1. The former will not be impacted by this, but COS approval will be dependent on this. USCIS may ask for proof of status b/w Sep 12, 2016 and Oct 1, 2016. You will have to file H-4 extension and get its approval first and then submit that as response to potential RFE from USCIS.
I got my problem solved i.e I got my i94 with new dates as per the latest h1b petition of my husband by sending an email and the required documents to the CBP(suitable for me). They issued me an entirely new i94 within a day.