H1 is expiring, applied for COS to F1

My H1 is expiring on 27-Sep-2013. I am in my 6th year of my H1. I have applied for my I-140 which needs get approved before I can apply for H1 extension.

To be on the safe side I have got an admission in a university here and I have applied for COS which is currently in progress.

What are my options if my I-140 gets approved after 27-Sep-2013?

Do i need to wait for my F1 COS to come throgh before I can apply for my H1 again ?

If I leave the country to get my H1 stamping without my COS getting approved, will that be an issue?

Please provide your suggestions.