It's possible that you will be affected....particularly if the EY flights were issued under AF/KL flight codes which will no longer exist come October, meaning your ticket would have to be reissued. Given that they will apparently no longer even interline, it may not be possible to simply re-issue them under the native EY codes.

When China Airlines terminated their codeshare on AF flights between CDG and TPE, CI emailed me to tell me they had to reissue the ticket...which they did using the native AF flight codes...but as they were still alliance and interline partners it was possible to reissue the ticket by simply switching to the native underlying AF flightcodes