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Your H1b will be approved if all documents are in order. However, if you applied with a COS, then it will not be approved and you will have to go for a consular processing and get your visa stamped prior to start working on October 1st.
Get all your paperwork ready prior to leaving for India. After returing you can update the packet with new I-94. The packets will not be accepted by USCIS before April 1st 2017 when officially the H1b processing starts.