I found the issue. The site will seemingly randomly break. I tested by disabling all of my plugins to check for a conflict and discovered as I re-enabled them the plugin would stop linking to my custom page and products.
This has to be fixed by checking Disabling Default Pages option, saving, unchecking Disable Default Pages option and saving again.
This seems like a really flaky fix to a pretty big issue. If we have to hand the site over to a client for them to manage it might be an issue.
Does anyone have a suggestion on how to correct this or will this be addressed in the future?