I used to be able to upload my own .htaccess file to my root folder and configure things with it, but now when I upload it on my new vndv.com domain, it gives me an error page and won't take me to my website. If I delete the .htaccess file, my website re-appears...

Are custom .htaccess files not allowed anymore or is this just a bug?

They are allowed but only certain functions.

Check the .htaccess sticky for an idea of what people have used successfully.