Unfortunately not — it's all or nothing here.
But could export those, than import them back after stripping all of both the Nero and QuickTime chapter info.
This is what I was thinking.
You can get a free trial of Fission (Mac app that costs $30) and save the .cue. This will also export a chapterless .m4a. If you want to spare yourself a step, go ahead and change the extension on that to .m4b and you can use that from here on. Load your chapterless file into FooBar, then right click > Utility > Edit chapters and import the cue.
That should (hypothetically) leave you with a file with only Nero chapters. However, FooBar seems to also strip most of the metadata when you do this, as when I load the file into Mp3Tag after that, the metadata is missing. If this happens, you can use "copy tag" before you do anything else to the file, and then use "paste tag" when you load it back into Mp3Tag.
Okay. So I wasn't able to use Fission with Darling or find a way to use a Mac that I could install software on, but I spent some more time searching for a solution and trying things. It looks like the newest version of fre:ac is supposed to be able to export a cue sheet, but I could not for the life of me figure out how. However, I did find a solution to my problem. It's not ideal, but until Florian gets a chance to implement QuickTime chapter editing into Mp3tag, this is the best I can do on Windows or Linux. For anybody with a similar problem, I'll explain what I did.
- Make sure all the m4b files you want to remove QT chapters from are in the same folder and have Nero chapters. If they don't, you can add them with Mp3tag.
- Make a copy of this folder.
- Load the original folder into MediaInfo and export a text file.
- Run the python script I wrote here with the name of the text file you exported as an argument. It will create a cue sheet for each file you loaded into MediaInfo. (Note that a cue sheet will only be created if the file already has both Nero and QT chapters. It will skip any that only have one type.)
- Open the folder with your original files in Mp3tag. Strip the mp4 chapters and remove all tag data.
- Load each file into Foobar2000 and right-click Utils -> edit mp4 chapters. Load the cue sheet created by the python script. (As far as I know, this step has to be done individually for each file. This is therefore the most time consuming part.)
- Load both the folder you've been working on and the copy of that folder you created in step 2 into Mp3tag. Order it by Filename. Then order it by Path. You can now select your copied files, copy their tag data, and paste that data into the newly altered files without QT chapters.
At that point, all the files should have the same tag data and Nero chapter information as before, but without any pesky QT chapters.
Thanks to Nolaine and everyone else who helped me with this.