In the places listed in /usr/lib/x86_64-linux-gnu/opera/resources/pepper_flash_config.json.
Due to some personal problems this week, I do not have the time to search and troubleshoot the flash problem on opera 49. I will when I can, because I also get the
Sorry, Flash Player is either not installed or not enabled.
message on adobe's page. My pepper flash however is on /usr/lib/adobe-flashplugin/libpepflashplayer.so so opera probaly identifies it, but for some strange reason it does not use it.