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the $HOME notation refers to your home directory, not the very top level of the boot disk. There is (still) a /Library/Application Support/Omni Group/ folder in the top level of the disk which contains the software licenses folder (which is unchanged). I think perhaps you ended up going there on the first attempt. The licenses are usually a per-computer item, so they don't get put in an individual user's home directory, unlike the stencils, templates, and other things.

Glad to hear it's all squared away, even though I've never touched a machine running Lion :-)