Check engine light will not shut off

It might be your scanner - cheaper scanners can sometimes give you trouble clearing permanent codes even once fixed if they have silent communication issues. You probably need a better scan tool. The ones I have had good luck with on difficult codes are usthe Innova 5610, the Xtool IP616* (I have the V1 with limited bidirectional support as it was added to my pre upgraded IP616) and a fully bidirectional Vdiagtool. You want one with eOBD OEM codes.

This still kind of works but on ~2015 and up, not as much for emissions codes and such (even borderline P codes) due to the EPA but sometimes the pull the battery for 30 minutes trick still works for "active" and "history" codes. It isn't as effective as it used to be but it's still a option.