Just to throw in my two cents;
It's important to remember that just because your water looks clear, and smells fine, is not indicitave of whether or not your water is clean. I'm sure you got that when you had that brief clean spell TubOguts!
As to the filter, I'm not so sure about re-using it; after all, part of the reason you replaced the last one was due to this very problem. It would just be unfortunate to go through all this effort to sanitize and clean your spa, only to have the mold reintroduced through that filter.
Regardless, best of luck to you with your tub and the clean!