I have a website built with Wordpress that has been having permalink issues. A few days ago, I had added a simple file, named qr.php, that I dropped in at the root level (where the wp-content and wp-upload folders reside). It has a script that redirect to pages outside of my website depending on what type of device the user is using. Basically, some one on a Apple device gets redirected to an itunes page, and droid user to the droid app store, etc.
Could this non Wordpress page be causing issues? I have had static or html pages in amonst my root level files before, and never had an issue. I feel like the redirects may change this.
Rather than using the qr.php(cutom redirect file) in your wordpress site. You can use a plugin which will help to redirect the external links.
Some of the plugins which might help you to achieve your purpose are Device Redirect - WordPress Phone &Tablet Redirect , RedirectPlus - Wordpress Mobile Redirect Plugin.
See the screenshots, try demo and check whether it fits your requirement.