I'm having the same issue that you. Some projects i use the iso-8859-1 encoding for all the files, and for other clients i use utf-8 (depending on their demands).
Since i set the default encoding in st3 as utf-8 when i open the iso-8859-1 files i have to go to file > reopen with encoding ... otherwiser i can easilly fuc* the entire file ....
how can i solve that ? Could st3 auto detect the encoding of the file ?