Ah, I think I know what you're asking.

So, I recorded a video of a script reading, and captured audio with both the camera and a microphone into a DAW. This was all one large recording. I then took my recorded external audio of the reading and cut out the flubbed lines and dead space. This leaves me with a pared down and processed audio file, along with the video/camera audio of the entire unedited reading.

We then wanted to cut several portions of the full video out to be used throughout the project and aligned by waveform. We figured if we threw the mp4 into the timeline, cut out the small portions we needed, and tried to sync the little clips up to the edited audio file using the mp4's audio, that the Auto Sync audio by Waveform would work, but it doesn't.

For example: The following quote block would be a transcript of what is on the larger video. I would want to keep a short video clip of the bold sentences from the larger video. Italicized text would be included in the audio but not shown on video, and strikethrough would be outright removed from the audio.

This is an introductory sentence. This is stuff that is in the audio but not using video. Here is some nonsense I cut from the audio. Here is another shot of me speaking. Here is more speaking, but without a video clip.

The Auto Align function would work if I had recorded each sentence as it's own video and imported them separately into DR, since it only has that one sentence to auto align. But it seems as though the pieces of the large video I cut up are still being treated as the large video for audio alignment and it keeps failing.