I'm pretty sure he's doing that procedure, manually at the shell prompt, already. His problem is (if I'm reading him right) that he does that procedure, and it fixes the problem once. Then the next time he synchs with Emplode, the problem returns.

His theory is that it's because he's got so many songs that the database is too big, and it passes the Emplode timeout for database rebuilds. I'm not sure that's true, but certainly something is going wrong here, above and beyond what that FAQ entry covers.