Hey there,

I am really sorry for the delay of this reply as it is a weekend for us here.

Yes, that auto update will not work for this version when you try update from Komento 3.0, it required to download the latest launcher installer from https://stackideas.com/dashboard then upload through your backend installer page and proceed that installation.

1. Assuming I should remove Komento first and then reupload the zip file.

You actually do not need to remove anything from your current site, you can just follow my above instruction to update your site Komento version.

2. Will doing this remove all my existing comments?

For this installation will not touch any of your database Komento existing comment data, it will just override all the Komento core PHP file to latest file from your site, if you have do any customisation from your Komento PHP core file then you have to do the full backup first before you perform this update.