If I update Vivaldi is the existing bundle.js overwritten?
No, but it's not used as well.
Vivaldi keeps two folders in its installation, one with the latest version and another with the version you had. When you update Vivaldi it will install all the new files in a new folder with this version number and your old bundle.js will be kept in another folder with the last version number.
There might have had changes in bundle.js, so you may try a diff, but simply restoring it, is definitely a bad idea.
Hmm…that's a pity. I have done some mods to bundle.js to allow my Speed Dial 2 to run. I can do it again but I wouldn't want to have to do it for every snapshot.