It went from 64 bit OS to a 64 bit OS, so that shouldn't be an issue. Even made sure RRD tools and the processor architecture were both 64 bit, and they were. I'm not sure what you mean by incompatible graph definitions. This 4.2 server got all of it's data and templates directly from the 3.1 server during the upgrade.
What I did to upgrade was install zenoss 3.2 on a fresh RHEL6 server (Using hackman's RPM).
I then copied over Data.fs, the $ZENHOME/etc directory, and all plugins we use (ldap mainly), and made sure zenpacks were all over.
Then I upgraded up to 4.2.3, then to 4.2.4 once it came out
So graph definitions shouldn't be any different.