One of the things updater 3 does is change the underlying compiler in CFMX. As such, the installer needs to clear out all the existing compiled class files in the cfusionmx\wwwroot\WEB-INF\cfclasses directory (note that's cfclasses, not classes). The good news is that the installer is supposed to solve that problem by simply renaming your current cfclasses directory to cfclasses_backup.
There are a couple of ramifications of this to be aware of:
1) this means that all first attempts to run CF templates will experience the delay of compiling (which happens only once when code is created or edited, but now needs to happen this once because to CF, it appears to be new code)
2) MM points out in the release notes you can help alleviate that burden by precompiling the code. This is new, as previously the only precompilers were those that folks passed around to each other (as I have in the past). They discuss this issue and their compiler in the release notes, specifically at this point,
3) The precompiler they use is pretty simplistic. It only compiles code "under the web root". That may not suit you. So I have a more complete compiler in my 12/10/02 entry.
4) If you experience any strange errors, it would probably be safe to simply rename the cfclasses directory or delete it (while the CFMX service is stopped). On restarting it, CFMX will create the cfclasses directory when you first execute a CF template.