I have been investigating this for a couple of days and I can't find an answer. I licensed Extension Builder 2 and am a Creative Cloud subscriber. My ideal scenario is to build my extension with Fb 4.7. However that seems an unsupported configuration so....
My second best option is to build with 4.6:
I install CS Extension Builder 2.0 into FlashBuilder 4.6.
Install seems to complete.
I build a simple helloworld project.
I target for CS 6.
I select Run As Adobe Indesign Extension
I get the error: Unknown Flex SDK: "Extension Builder 4.5"
Sure enough, my project is targeting "Extension Builder 4.5" but this SDK is not installed. Or not recognized. Or...
Please help. I have encountered this on two separate machines (both mac os 10.8.3) and I am stumped.