You could, however if a button was mapped to Flirc and the function on the tv setting you were using then it would cause both to react.
For example:
You set "channel up" button on your remote to Stop button in Flirc (for a media app) - this would cause the channel to change and Flirc to stop the video the media box was controlling.
An optimal situation for Flirc would be to use a remote that would be used at the same time (e.g. a DVD remote - if you used it to control a media centre and a DVD player it is unlikely you would have both machines on at the same time)
or
A multi-remote such as the logitech harmony remote (or most other remotes)
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