Hi
Johnny. The command
Process>Apply Effect>Gain is destructive. ie It is like Audio Suite in Pro Tools. Any changes here are permanent. You only have one level of undo and that is immediately afterwards. Once you save the session I don't think you can go back in Sonar and undo these commands.
This process will alter the audio in the original recording and the waveform in view. It is not bad certainly as long as the changes are good and sound good and don't add distortion or anything to the original sound.
If I knew I was going to be doing a lot of this I would
clone the audio track that represents the audio you have recorded and rename it in such a way that if all failed I could revert back to it. Edit the copy or the original but have the other as standby.
Then you could alter the various parts of the audio track using this permanent command. It is only bad if what you do ruins the sound for any reason or sounds unnatural. But in the end it is better to not alter the audio in anyway way if possible.
Clip Gain as per Studio One/Pro Tools etc does not change the original waveform in anyway. Just that clip is altered and played back at a different volume. The waveform visually does reflect what you are hearing and seeing etc. So it is better from that point of view.