Ok, migration can't be done via Flash Pro because it require command line complation access. But this can be done easy. I hope your OS it's Windows? )) Because I don't use a Mac.
adt -migrate -storetype pkcs12 -keystore cert.p12 myAppIn.air myApp.air
this string can be executed easy.
1) Locate your Adobe Air SDK and copy it's path to clipboard.
2) Create somewhere folder and put your original.air there
3) Create Migrate.txt file
4) Type in it:
"C:\Program Files\Adobe\Air Flash Runtimes\4.0.0.1390\bin\adt.bat" -migrate -storetype pkcs12 -keystore cert.p12 original.air update.air
Change full path to your Air SDK location. For example it can be like:
"C:\AdobeAirSDK\bin\adt.bat" -migrate -storetype pkcs12 -keystore cert.p12 original.air update.air
5) Rename Migrate.txt to Migrate.bat and execute it. ADT may ask your certificate pass. Type it and press enter.
I never doing migration because I use only Embeded with *.exe inhouse distribution. But using link you provide - you can do it yourself. Just change everythere adt to "C:\AdobeAirSDK\bin\adt.bat" your any other your sdk location.
But I always use ADT in command line 
Hope this helps. But this is for Windows. I don't know how to deal with MacOS command line.