I did something stupid. The empeg was connected over serial and I told it to sync something like 1.2g. Realizing that I wasn't using ethernet, I de-pwered the unit (the cancel button wasn't enabled) After it powered up and I got it configured to use ethernet, I erased the playlists that it had downloaded, and started the sync again.

Everything goes well until all the files are done. Then I get a "operation not permitted" message and the payer is locked in the syncing screen. I power down the unit again. It comes back up ok.

What state is my machine in? What actions should I take?

If it's working OK, then you don't need to do anything. Perhaps run a do-nothing sync to ensure that the database is rebuilt correctly.

The cancel button is never enabled, so don't sweat it.