I don't use NME, so i'm not sure how this fits into NME's build tools, but with plain haxe you would use a build server, eg:
haxe --wait 4000
to start the server, and then when building, add
--connect 4000
For as long as the build server is running and being used, the compiler will cache the results of compiling modules, so things like nape will only be compiled the first time round, and for as long as code is not changed, the only thing compiler will do is generate the .swf