First of all: Thank you for your wonderful program that's served me so well all these years!
Mp3tag currently creates Nero metadata for any MP4 file with chapters, but also writes to the standard metadata. This seems fine in theory, but apparently, it also means that Nero copies are created for every standard metadata tag that's set in that file, meaning that if the standard tags are changed with another program, Mp3tag cannot see the change, and the unchanged tags remain in the file as “ghost tags”.
Take this example file – It was created with the following steps:
Create an MP4 file with chapters.
Use Mp3tag to set all the tags to “Set with Mp3tag.”
Open the file using Mutagen and overwrite all the tags with “Overwritten with Mutagen.” (This issue applies with any other tag editor I've tested as well, e.g. AtomicParsley.)
This results in a file that Mp3tag thinks has the original tags, but every other tag editor and media player only sees the updated tags for. (The second screenshot is from ffprobe.)
There was a thread about this back in 2022, where the status was that it wasn't possible to suppress Nero metadata creation when an MP4 file contains chapters. Given this “two unsynchronized copies of the metadata” situation, however, perhaps it should be off by default?
This is essentially stopping me from using Mp3tag entirely at this point, unfortunately… I have to use other programs (which don’t read or set Nero tags) to edit parts of my files’ metadata, so if I use Mp3tag, I always end up having a desynced, incorrect copy of all the metadata in the Nero tags which is all that Mp3tag will see. (Plus, I haven’t found a way to remove Nero metadata, even using other software…!)
What happens if you change the settings option to untick m4a chapters? You will have to close mp3tag after changing this setting, then reopen it and the same file as well. Can you then see these unchanged tags in mp3tag?
Unfortunately it seems that the standard m4a tags and the Nero tags that allow chapter naming just are not mutually compatible. I have found the same when using mp3tag to update concert videoa and add the song namea as the chapters.