I have an old WHM/cpanel server running on RH 7.3 or 9, I can't even remember which (think its 9). I have used the backup feature in WHM to backup all the sites. If I now get a new WHM/cpanel server thats running RH Enterprise can I simply ftp the files over, use the WHM restore feature and end up with all the sites moved to the new server? I think it should work in theory but has anyone tried it in practice?

Just make sure and upgrade WHM on the old server to the latest release (stable/release/current any will do) and let the backups be made by that version.

The transition between 7/9 and RHEL will not give you any problems.