Just like having your favorite TV show cancelled, features and products get cancelled because there isn’t evidence of enough usage to pay for the cost of development.
You can use Flex 4.x for the forseeable future. There is no official support for combining FB4.6 and FC5.5, but if it works for you now, it should keep working forever. Just be careful about offers to automatically upgrade the products, and back up your installers just in case.
Adobe seems to be making all kinds of stupid decsisions these last couple of years. My personal opinion, the idea of Flash catalyst was better than the actual app. I found the app to be clunky, incomplete, unusally difficult and had a completely opposite workflow compared to applications like Fireworks. I also thought that Adobe really missed the ball on know who their customer actually was and what software they were using prior to Flash Catalyst (Fireworks and Flex). All old news at this point.
Even though it is not the same, here is one alternative you can use for simple prototypes - http://uiblueprints.com/demo/index.html
It lacks skinning capabilities but it actually has a much bigger component library than Flash Catalyst had.
You can find the answer. Just modify some config file.
In Applications/Adobe Flash Catalyst CS5.5/plugins/com.adobe.flexbuilder.flex_22.214.171.1248731/config.xml add in a reference to 4.6. You’ll need to copy 4.6 into the sdk directory. When you publish it will publish with the 4.6 SDK. Still haven’t figured out how to add new components to the components panel or change the theme (mobile) (or add new Interactions…) You can export this project and import it into FB. Going the opposite way is a bit more trouble. You’ll get an error about the supported SDK’s. You may need to update the hidden project files to “4.5″ instead of “4.6″ which may allow you to import it again… There’s more you can update… search for plugin.xml in the plugins directory.