I have a problem with changing lower_case_table_names variable value in MySQL 5.6 ... I did all that says in Where to change the value of lower_case_table_names=2 on windows
I solved this with a file I found under
C:\ProgramData\MySQL\MySQL Server 5.6\my.ini
So, it was ProgramData, not Program Files. I got this path from MySQL Workbench -> Manage Server Instances -> [tab] System Profile -> Configuration File. Guess this is the place where one should look for the current config filepath.