Hi Juraj thanks for the quick reply.
It's a hero banner widget and the URL selector form component. The custom module is registered in the Webapp solution following the documentation, but I wasn't aware we had to register the module in the frontend app too. Required configs are present in both apps and azure variables.
I have now disabled the media files sync checkbox in webfarm settings and will update here if the issue persists.
Edit: Eg. I uploaded a new image to a folder in media libraries and I can see the image is present in the correct azure storage container. It also appears in the media libraries view in the Administration app. The getmedia endpoint works when going through the backend domain eg.
app-site-backend-dev-01.azurewebsites.net/getmedia/295b2391-497b-4747-987d-765e77fc03c6/image.png
But the same endpoint just pointing to the frontend, throws a 404 error
app-site-frontend-dev-01.azurewebsites.net/getmedia/295b2391-497b-4747-987d-765e77fc03c6/image.png
Some additional info, we haven't actually deleted the media files from the Web App itself, could that cause some issues? Also, after creating a new folder and adding an image to it, we verified it works and shows in the media libraries page in the CMS, but when trying to load it via the page-builder it throws an error saying it can't find it.
The getfolderstructure request fails, with an error in event log saying it can't find a part of the path like I mentioned in my initial question.
Hopefully this gives a clearer image, if you need any more info please let me know.