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Other parts of your system very likely require the apt ffmpeg. Keep it, or at least note the packages that apt wants to uninstall because they depend on ffmpeg
You cannot run flatpak application by simply calling the binary.
Coming to your question, I suggest you to install ffmpeg directly from your Debian repo, this way you can get hardware acceleration or device specific benefits for encoding/decoding/transcoding.
You can keep the flatpak version if it is needed by some other flatpak applications. Normally one won't interfere with the other.
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