Hello; I started keeping tanks back in 1959. I went from no filtration to UGF to UGF with air powered HOB's. For a number of years I had not learned of doing regular water changes. The point of this post is to put into some perspective my experience with removing a lot of gravel.
Because I was not cleaning gravel as I now often do by siphoning it out during water changes, the substrate would become loaded after a year or two to the point that a tank tear down was needed. UGF does not remove detritus at all and the early HOB's were not very effective at it either. I also over stocked and over fed .
While I would try to catch the fish and put them in a bucket, there were often a few that could only be caught after much of the water and gravel was stirred up. By that time the water was so thick with detritus that I could not see thru the tank. I am sure this was not the best for the fish but they faired fine for the most part.
Were I to do what you plan, I would use a siphon hose large enough to pull the gravel thru. I would do enough 50% water changes to remove all the gravel even if it took a few sessions. This method has worked for me several times and stirs up very little detritus in the process.
About the concern for the beneficial bacteria (bb) being removed with the gravel. My take is that you have three four inch fish only which should not be a big bioload. They are messy eaters so the reduced feeding suggestion is not a bad idea. I also think that the bb are on surfaces throughout the tank. The colonies on the other surfaces and on the filter surfaces and media will remain established even when the gravel is removed. I also suspect that many bb colonies will be located along surfaces where there is some water flow. If you do not run a UGF there should not be much flow thru the gravel. My guess is that the bb in the gravel may be living more off of the decay products from excess food bits than from excretions from the fish.
On that bb in the gravel note. Back in my "dark age of tank keeping", I would take the dirty gravel out and give it a good rinsing with a hose. I would then put it back into the tanks right away along with fresh water and the fish. No problems and this annual cleaning perked up both the fish and the plants. My take had been that the bb are tough and tenacious.
I was puzzled about statements in posts when I first joined online fish forums. It was often stated that the filter media should be gently rinsed in a bucket of old tank water to avoid losing the bb. I have hit the filter parts and media with a garden hose for years with good results. I do not scrub the surfaces, just rinse them off. The slimy layer clings well.
I have read post where folks are reluctant to change the filter media at all. I put new media into my HOB's any time the need arises. As long as The other parts of the filter are not scrubbed at the same time there should be bb on the surfaces. There will also be bb on other tank surfaces.
My contention about the bb clinging well was also mentioned in an article. I may still have it saved and should be able to post a link to it if anyone is interested.
Good luck with your project.