Hi,
The issues you got with the update install is because of your server restrictions not letting Joomla enough time to process the install package.
I've never heard of a duplicate HikaShop after update. In fact, it's just impossible to have two HikaShops on the same website. We've had several people asking us to install two HikaShops on the same website, but the way Joomla and HikaShop are done, it's not possible to have two different instances installed together.
So I'm thinking that there might be some caching issues or something.
Try to clear your browser's cache and logout/login from your website backend. Then, in the HikaShop configuration, click on the "check database" button in order to make sure that everything is correct in the database.
Then, check if everything is ok.
If not please provide screenshots of the issues. If you really want an only version, you can request it via our contact form, but I doubt that it will fix anything. We did update tests before the release and they never shown that problem so you should get the same result with the 2.5.0