You can try to remove the offending parts from the file manually with a text editor. Go to the line and offset and try to decipher what it means. But depending on the file there may be tens or hundreds of similar items, in which case you have to use some advanced find&replace functionality.
It would be possible to make a python or other script for this but I haven’t heard about any. The developers have explicitly told that backward conversion won’t be supported in KiCad itself.
You might find that removing the stackup section and maybe changing the version to 5.1.6 with a good text editor (NOT Word) might be sufficient - I am away from my computer at the moment so can’t check.
The file format going forward will continue to change and even if there is a script that works now, it will probably break with the next format change.
You can run 5.99 alongside 5.1.6 so, depending on the risk you want to take, you might be able to finish your project in 5.99. As has been pointed out, the 5.99 versions are really just for testing and not for production.
