I would really try and avoid this... In general, Red Hat don't even support upgrading from one version of AS to another (e.g. 2.1 to 3), so it is highly unlikely that an upgrade from a non-AS version would work.
Filesystem issues aside, you would most likely be left with binaries from RH9 RPM's lying about, and I think some of the RPM dependancy chains may have changed as well.
Red Hat recommend a complete reload when moving from one major version to another, and I don't think that they will support AS unless it has been installed from scratch.
This is, to my mind, still one of the biggest stumbling blocks that the so-called enterprise linux vendors need to overcome. It is not reasonable to expect enterprise organisations to take machines out of service, remove all applications, re-install the operating system, all applications and all data, and then re-insert the machine into service.
FreeBSD gets around this beautifully, so I'm not sure why the big boys in Linux land haven't got their act together on this one yet