After Effects CC 2014 (13.0) and later no longer include exporters for creating files in the Flash Video format (FLV and F4V). Adobe instead focused its efforts on the H.264 (.mp4) exporter, which is currently recommended by the Adobe Flash team.
You can still import videos in these formats into After Effects and Adobe Media Encoder.
If you want to create a video to play in Flash Player, use the H.264 (.mp4) format, not the obsolete FLV or F4V formats. This has been the Adobe Flash team recommendation since Flash Player 9.
If you still need to create FLV or F4V files for legacy workflows, leave After Effects CC (12.2.1) and Adobe Media Encoder CC (7.2) installed alongside the current versions and use the previous versions for these specific output tasks.