Had the same problem (but not with custom meta data of type RTF). The only thing that helped to get completely rid of the meta data was to delete it from every record. However, I used a scripting addition that doesn’t work on current macOS versions anymore.
So I think your only option is to try whether Script: Remove some custom meta data also works with custom meta data of type Rich Text. I did not test the following limitation with this new script:
Due to an AppleScript limitation it’s not possible to remove meta data of type
rich text.
Reading the script and its description again now I don’t see a reason why it should not work.