I'm slowly piecing things together: it looks like you can have a Haxe project target hxcpp as a library (dll, so, etc), perhaps by hand, perhaps using a BuildFile.xml, and the workflow for loading and using these libraries is called FFI (or CFFI? C Foreign Function Interface). You can load (and unload, as Hugh points out) these libraries at runtime, presumably either unload/overwrite/reload or overwrite/restart, to upgrade your application.
Some source links:
http://old.haxe.org/doc/cpp/ffi?lang=en http://old.haxe.org/forum/thread/3395#nabble-td6179190
Of course, this complicates the build (and makes profiling more opaque inside cffi.)
A wrapper application certainly seems a little more straightforward, but I haven't had great luck getting a wrapper application to launch and get out of the way properly on the Windows platform - e.g. I had a splash screen as a separate app, and while it worked on Linux, on Windows the first stayed open until the second was closed (something about forking the process.)
Then again, I suppose a wrapper app complicates the build (and potentially user experience) as well.
Hmm, I'll keep mulling this in the back of my mind.