Hi Bill,
This is always how I do it, by smoothing the nib. I do tend to try and take of the baby bottom first, by just smoothing the part where the baby bottom occurs, and then do a general smoothing.
If a baby bottom is so bad that you need to reshape the nib, it needs to be sent back to the supplier.
Also, a baby bottom may occur as a partial baby bottom, i.e., only at a specific angle, and most of the time, the angle you personally are writing at, and nobody else

. This is dealt with in the same way, but you would only fix that particular point, and then smooth the whole nib again. BTW, I did find a nib once with 2 partial baby bottoms

.
For fixing baby bottoms, I use 1 micron (approx. 8000 grit) and 0.3 micron (approx. 12000 grit) mylar, just as I do for smoothing nibs. And this shouldn't damage flow characteristics, if you do it properly, i.e., carefully, softly and smoothly.
HTH, warm regards, Wim