Well, today I was doing some experimenting and investigating how I could get my Tracker application published to a subdomain through automation instead of manually copying the files every time. It’s only an MVC template right now but I wanted to be able to test that the default functionality was going to work with my web hosting, prior to proceeding. Things were going pretty good until I realized that publishing my application broke my WordPress site. By broke what I mean is that critical files and settings got overwritten causing my site navigation menu to get messed up as well as links to pages not working (404 errors) and only my home page could be displayed.
I hypothesized the cause of the overwrite to be due to the subdomain folder being contained within the root folder for my website instead of up one level so I deleted the subdomain and the folder it was using. I then recreated it so its root folder is at the same level as my main sites root folder. Apparently trying to organize your subdomains within your root domain folder is not a good idea.
I was then able to follow the steps again to publish a web application, which I outline here.
I took the opportunity of my site already being broken to install the latest WordPress update.
Since my incorrect publish broke my custom links I determined how to fix this was from my WordPress dashboard you go to Settings -> Permalinks and switch the option to Default and save your changes. Then you switch it back to your custom selection and save the changes again. Prior to discovering this not even deleting the pages permanently and recreating them removed the 404 error for me.