I see two issues: the first being the mixed SD and HD material and the second being the fact that you don’t want to redo all the work to define the chapters
Another problem is that you cannot “trust” PD to correctly render SD based material for a HD disk (larger files). Correct?
To change the disk creator to handle 4:3 material better is something you have to ask CL. There are some options setting the video format, and there is the smart fit, which allows PD to select the bitrate; but that is about it.
W.r.t. the chapters, I understand that you have set these chapters in the disk creation step. I don’t know of a way to preserve the chapters if you redo the project.
I assume that you want this disk production to be perfect and last at least until your golden wedding celebration, with likely more work, I would recommend the following:
- Look at your SD and HD collection of videos that should all end up on the disk. And group the videos you want to keep together in the end product. Maybe that is “just” the wedding and the silver wedding, but it may also have a different grouping like, years, or family, etc. Then make a project per group of videos. It is handy to keep the SD videos together, but that is only if you want to prevent that a mix of 4:3 and 16:9 material alternates on the screen.
- Aim for a HD disk in all projects, so set them to 16:9. Do the “normal” editing in the timeline, delete the unwanted, apply transitions, titles etc. and…. Maybe you have done that already and can reuse it. Also define your chapters in the timeline. Once defined in the project, your chapters are preserved and available in the disk creation process. I can imagine that this approach already takes care of some of the chapter settings, because you already have grouped at project level? It is at least something to think about. What do you want with these chapters and more importantly: how will the disk-audience use the chapters (if at all). (Maybe you can make a screen shot of the chapter list in your old disk content list, so that recreating will be easier?
- For the SD material, likely in separate projects, you also set the project to 16:9, with the black bars left and right (you can change the color by using color boards, or change the background in other ways, if you want to.) My experience is that with SD video you also may need to improve the video quality a bit with color enhancements, denoising, etc. Experiment with applying a LUT to the material. You can both set the coloring and the ambiance in one go, which might make the material look more attractive?
- Save each of the projects (now containing chapter information), and give each project a name that will help you during the disk creation process: by year, by type or the like.
Then start the disk creation process and include the above projects, with a HD (Blu-ray?) disk as output.
It may involve a lot of extra work, but maybe you can reuse much of your work?
Hope this make sense and helps you a bit.

I would put the sd 4:3 ar content in a 16:9 ar frame and produce it at the final resolution and format chosen but reduce the bitrate to 8 Mbps. This way you can save the space wanted. For example, I used 1080/60p(28 Mbps) settings almost all the time. You can bring back this produced footage to the timeline and add the chapters and you will save the space. This works along with the HD footage that will be rendered at the 28 Mbps. I create 6 to 10 hr. BD in a similar way.