Any thoughts on whether it's safe to unplug the empeg when it's only half-way through synchronizing itself?

Your best bet is to leave the empeg running, but disconnect the ethernet cable. Then terminate Emplode and restart the computer.

Eventually, the empeg will time out and mount its drives read-only again (I think, not certain). I don't know how to tell when it's really done this.

I would then do a FSCK and afterward use Emplode to tidy up the errors.

After that, synch the few albums you know you can't live without...