The answer is simple: You don’t. You just don’t render anything as video. Period. If anything happens and disrupt the process, you lose everything! Even, without being so dramatic, if you want to redo a few frames because you notice a tiny glitch, well, good luck with your video.
Instead of crying on the spilled milk, you render what you need as images in a folder. It doesn’t matter if it’s 2 scenes in one file or the other way around and everything in between, you render as frames, each part in its own folder. When you have all your frames, you press [CTRL N] to clean the place and you switch to Video Editing.
You replace the (useless) Graph Editor with Properties which will show the Render tab. Click “Image” from the bottom “Add” menu and add all the frames for your intro, outro and the video in the middle. (Select all the needed images in each dedicated folder.) You align everything, you add a soundtrack eventually, you set the video size, format and number of frames… Then you can click the big Animation button to render the final video.
Of course, you can render just the intro or the outro to see what they look like before to build the whole final video… BUT! Don’t lose your individual frames until you’ve checked, double-checked and triple-checked the final video.
Edit: I forgot about ffmpeg. Well, if that’s what Blender uses to make the video, good… If not, who cares?