I think you should follow the factory maintenance procedure on something
like a transmission.

If it's an automatic transmission, I shy away from flushes.  I have a
Honda for which the factory procedure involves draining and refilling
the thing four times in succession, driving around a bit in between to
cycle the new oil in.  This gets a good bit of the old oil out.

I have a Lexus that some corner gas station did a couple of transmission
flushes in; 10K miles later, the entire transmission needed rebuilt.  
The previous owner did all this, and I inherited (quite literally) the
problem.  That's why I shy away from flushes.

It seems to me that modern automatic transmissions are incredibly
complex, perhaps too much so, and that shade-tree mechanic concepts
don't apply.