You said your flex application which is hosted on Azure is referring to the IIS and PHP on my local development machine.
How did you know it is referring to the IIS and PHP on my local development machine?
If the web role contains both the flex application and PHP scripts, once the web role is deployed on Azure, the flex application will be referring to the web role on Azure. I'd suggest you check the source code of the flex application and find out which
address is actually being referred.