I don't really now the exact process, but part of the problem is that taxonomists don't agree. It's is complicated procedure especially when you get into groups of fish that get reclassified. There are other issues as well, such as in the early years; late1800's & early 1900's, often these specimens were described by people in labs while the fish were collected by others. When you find a jar with a holotype fish in it sometimes it is not the same fish, that we know today. These types of mistakes somes times don't get it corrected until later. Stauffer and Konings are trying to clean up a few of these in their recent research on the cichlids in Lake Malai. Their change is submitted and put before a reviewing board who excepts it or not.
The same things going on with Cetral American cichlids, 95 percent of the cichlids have changed many times. all of this has Been reviewed by peers, and some agree and others don't. Frontosa is a great example of a splitter going in and changing all the names of Frontosa, first off the hobby didn't, buy it. People refused to recognize the naming, and now Konings has totally blown smoke thru that one.
With all these complications who do you believe? That is the tough one. You have to research who is working on a particular species and find it if it is something you can visually see then you are all more apt to believe it. But when it comes to scale & ray counts,it is more difficult. Often how they eat and breed can effect their classifications.
I think that it is easier to pick a guy that you respect who is working with the type of fish you are interested in. for example in Lake Malawi and Lake Tanangyika the worlds most authority on the fish in those lakes is Ad Konings. All though this can be confusing at times, As long as we have fish there will be someone who want to change there status around. There is not much we can do about it, except to try and stay on top of it.
Over on the Cichlildae forum, there is a taxonomy section. You should go over and read some of those and I think it will help you understand it better.