How to create alpha videos now FLV / F4V support dropped from Media encoder

Now that Media encoder has dropped support for FLV / F4V has anyone got any ideas how you would create a video with an alpha channel for use in flash professional. With flash professional only really supporting the H.264 CODEC, I can't see any way possible to use transparent videos now.  I'm currently having to resort to installing an old version of media encoder to get back access to FLV.  Does anyone have any other thoughts on how I could achieve this using the latest software. 

Hi Preran,
Can you clarify why the Alpha channel video option has been removed?
There's all sorts of reasons why people still need FLV, in our case its the video format we use with Aurasma to be able to have animated text on a transparent background in an AR environment....
Why oh why would you just remove the option when h264 clearly doesn't replace all of FLVs features?

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