If I try to create a LaTeX file named notes.tex, AUCTeX automatically adds the style "notes" and runs the style hook for "notes". This creates a bunch of environments in LaTeX-environment-list that conflict with my custom environments. Is there a way to prevent AUCTeX from automatically applying this style?
Alternatively, is there a way to remove a style hook?
This is part of AucTeX's customization features. It's explained in the manual. I don't understand all the details, but it appears to include applying styles for files when the filename (in your case notes.tex) matches an AucTeX style file (i.e., notes.elc).
There doesn't appear to be a way to turn it off. However, you can customize the variable TeX-style-path, removing the directory containing the style files you don't want to use.
Someone else may be able to provide more complete help!
notes.tex?TeX-auto-savein that buffer?TeX-auto-saveis nilnotes.elwas generated. AUCTeX itself doesn't contain anotes.el, as you can see here. Maybe you've generated that last time you created anothernotes.tex? In that case, you can probably remove that .el file.