mclrobert I don't see anything in the theme source code that would cause this.
Do you have a backup of the composer.json file before you ran the command? The only way I could see this happening is if you had already manually removed all those other extensions from composer.json previously but just didn't run any Composer command in the meantime. Or maybe you manually copied or reverted the composer.lock file from a different backup that doesn't match with the remaining of your files.
To re-install the missing extensions you will have to add each one of them to composer.json (original list) and then run the update command as described in the update guide. Or you can re-install each one with the composer require flarum/approval:"*" command. You can add all of them to a single command like composer require flarum/approval:"*" flarum/bbcode:"*" flarum/emoji:"*" [etc]
If Composer doesn't let you re-add the extensions, you can run composer why-not flarum/approval ^1.6 to see if there's any other installed package that forced all those extensions to be removed.
