I can't say for certain with the S4, I had an Aviator that I had experimented with rooting and stuff. I had the "yellow" warning triangle after I had rooted.
When I was done playing and before I gave it to my step daughter to use I "ODIN" flashed the stock rom. The phone was just as if it came out of the box. No yellow triangle, just like new, and asking all of the "setup" configuration questions on start up. Language, country, etc.......