It doesn't seem possible to edit an existing prefab, as it won't allow you to save over the existing ".et" even if you override in your project folder. However, you can edit and then use that to create a new prefab, by dragging the parent GenericEntity, which should contain any Entity's you've added or modified, directly into the Resource Browser. You'll then be prompted to name your new prefab.
This post on the Wiki should explain this better: https://community.bistudio.com/wiki/Arma_Reforger:Prefabs_Basics
It's certainly odd that you can't simply "save" or "save as" to the Resource Browser if that is what's required, very unconventional at least for consumer software.