First of all, as Brenden said that you need to check whether there were errors while upgrading from 8.2 to 9? You may check logs for that.
How much is the custom code that your project has? Can you do something on these lines that what I did to successfully upgrade my website from Kentico 8.2 to 9 in like an hour.
Take export of all essential objects/Pages/Settings from your 8.2 instance which is in production working well.
Install Kentico 8.2 locally and import this website on that.
Run Kentico 8.2 to 9 upgrade utility locally. Make sure all is working well.
Resolve any code changes suggestions by the tool.
Now using Kentico content staging, sync your objects/pages between your local upgraded Kentico 9 instance and targeted server.
Copy your custom code using FTP to the targeted folders.
This solution assumed that you are using Azure Websites deployment model.
Let us know if this works.