I have experienced the same problem as AJ.
I needed to correct this issue but with woff and svg file types. I make the change and then flush all the cache in W3TC and then test in GT Metrix. When I test it gives me the same results as before. So I re-open the .htaccess file and it has reverted back to the W3TC version. E.g. with the SVG and Woff file types included in the section I am trying to amend.
Any suggestions on fixing this?