user21882: Say I have a video file with contained audio file. So a container with audio and video codecs.
If I'm applying an operation in ffmpeg that will re-encode the video, such as applying filters or changing the container (assume it supports the audio codec) or video codec or whatever, does this also re-encode or affect the audio of the output file in any way?
Does the audio codec just automatically get a kinda pseudo -c copy command applied and translated over to new video file?
I'm trying to understand whether I need to specify a -c copy for the audio every-time I do an operation to the video part. Whether for the purpose of speeding up the operation or for avoiding quality-loss.
Like when setting an audio input and a video input and combining you need to specify a -c copy to get it to simply combine them. But I'm just a bit confused if you need to worry about it once the audio codec is already safely in the container and I'm applying operations to this video afterthefact.

user17075: 
Does the audio codec just automatically get a kinda pseudo -c copy command applied and translated over to new video file?

No, use -c:v for your video codec, and then -c:a copy to instruct the stream copy of the audio stream.
For example:
ffmpeg -i "inputfile" -vf "filter" -c:v libx264 -crf 18 -c:a copy "output.mp4"
Another note about ffmpeg defaults: 
Not all things need to be explicit, only experience and reading the documentation gives you the best feel for this.  Notice that we had to explicitly specify the audio stream copy, yet in my example above, I haven't explicitly set -f mp4 container.  This is because the file extension of the output file (mp4) selects the default container for that file extension, which is something one may or may not want.

user1871: In ffmpeg, copy mode for -codec / -c always needs to be expressly set.
So for
ffmpeg -i in -c copy out

ffmpeg will perform automatic stream selection and copy all those streams.
For
ffmpeg -i in -c:a copy out

ffmpeg will perform automatic stream selection and copy audio stream. Video stream will be transcoded.
I suggest you read the above link on stream selection fully. It covers stream handling.

21882: <p>Say I have a video file with contained audio file. So a container with audio and video codecs.</p>

<p>If I'm applying an operation in ffmpeg that will re-encode the video, such as applying filters or changing the container (assume it supports the audio codec) or video codec or whatever, does this also re-encode or affect the audio of the output file in any way?</p>

<p>Does the audio codec just automatically get a kinda pseudo -c copy command applied and translated over to new video file?</p>

<p>I'm trying to understand whether I need to specify a -c copy for the audio every-time I do an operation to the video part. Whether for the purpose of speeding up the operation or for avoiding quality-loss.</p>

<p>Like when setting an audio input and a video input and combining you need to specify a -c copy to get it to simply combine them. But I'm just a bit confused if you need to worry about it once the audio codec is already safely in the container and I'm applying operations to this video afterthefact.</p>
 17075: <blockquote>
  <p>Does the audio codec just automatically get a kinda pseudo -c copy command applied and translated over to new video file?</p>
</blockquote>

<p>No, use <code>-c:v</code> for your video codec, and then <code>-c:a copy</code> to instruct the stream copy of the audio stream.</p>

<p>For example:</p>

<p><code>ffmpeg -i "inputfile" -vf "filter" -c:v libx264 -crf 18 -c:a copy "output.mp4"</code></p>

<p><strong>Another note about ffmpeg defaults:</strong> </p>

<p>Not all things need to be explicit, only experience and reading the documentation gives you the best feel for this.  Notice that we had to explicitly specify the audio stream copy, yet in my example above, I haven't explicitly set <code>-f mp4</code> container.  This is because the file extension of the output file (mp4) selects the default container for that file extension, which is something one may or may not want.</p>
 1871: <p>In ffmpeg, <code>copy</code> mode for <code>-codec / -c</code> always needs to be expressly set.</p>

<p>So for</p>

<pre><code>ffmpeg -i in -c copy out
</code></pre>

<p>ffmpeg will perform automatic <a href="https://ffmpeg.org/ffmpeg.html#Stream-selection" rel="nofollow noreferrer">stream selection</a> and copy all those streams.</p>

<p>For</p>

<pre><code>ffmpeg -i in -c:a copy out
</code></pre>

<p>ffmpeg will perform automatic stream selection and copy audio stream. Video stream will be transcoded.</p>

<p>I suggest you read the above link on stream selection fully. It covers stream handling.</p>
