Not in Flash Builder, no. You can do it in IntelliJ (I am in the middle of trying to make the switch right now and that has been a fantastic feature so far). If your ANE is open source, as quite a few are, it is likely the SWC used by the dev to compile the ANE is included in the source code, or you could generate yourself. The SWC is the only portion of the ANE required to compile any kind of AIR app or library. You'll have runtime errors if you don't include the ANE in the app, but that is a given regardless.
So if you have the SWC or can compile one, add that as an external library to your project.