How to completely remove jailbreak?

I have jailbroken one of my phones a while back ago, and while I am no longer in a jailbroken state, I think I have still have some excess jailbreak files leftover, as some apps are crashing upong JB detection. I also ran a test on the Certo Mobile Security app (though not sure if it's accurate/trustworthy) and it says jailbreak detected. My device is already at latest version and it wants to perform a restore from backup using iTunes.

But with the restore from iTunes part, what if I backed up previously when I was still jailbroken? If I restore from iTunes with that backup, will the JB files still resonate? I did some searching online and I get both answers saying restore from backup works and doesn't work, as well as a DFU restore will work.