I have done this before too and 1/2 of my fish died from something in the gravel probably. Sucking it out takes the gross stuff with it. It really works! I have the large size gravel and the bigger siphon hose but it does work.I switched from gravel to sand in my 20g last year. I did half and then a couple weeks later the rest. I did not drain the tank or take the fish out. It was a bit messy (gravel hides a lot of gross stuff) but worked out in the end.
Oh I've always been told that substrate holds a fair amount of beneficial bacteria. Allong with glass, wood E. C. T
There's lots of people who use gravel to seed new tanks so they are wasting their time?