I haven't done the flush yet (will do my first onethis week!), but have been doing lots of research on the flush - and from what I've heard a flush is not a one time cure-all; it seems like more of a liver-gallbladder management system. So, someone believes in going under the knife to remove these things will need to do it again. They WILL come back.
What makes more sense is preventative measures on a regular basis, i.e. diet or flushes; there seem to even be ways to manage on a milder versions of the flush...
I think what your surgeon is saying doesn't conflict with whether or not these flushes work. In fact, it's really good corroboration that people do need to take this stuff seriously!