We're trying to test a new navigation. In order to do this, we serve both navs and then using Target, we add a script to the test variant that hides the old nav and shows the new one. It's three lines of JS.
However, we've experienced both a flicker and it will go back and forth from test to control for the same visitor. Adobe told me to just do it through Visual Editor, but that would frankly be a lot of work.
Just to get more understanding of what you are doing, How are you adding the script that hides the old nav ?. However the ideal way would be add the code using "Code Editor " inside visual experience composer.