Some of the application types on Connect are:
- Shiny apps
- R Markdown
- Parameterized markdown
- Plumber
- Pins
- etc.
The only times I've seen encountered this problem is when I deployed an R Markdown, and THEN changed the same Markdown to be parameterized. Since a Parameterized Markdown is a different content type I had to deploy to a different endpoint.
It's not entirely clear from your post, but it seems you might be using Git backed deployment?
If you are using Git backed deployment, you should probably start a fresh deployment using the "Publish" button in the Connect GUI:

If, instead, you are not using git backed deployment, but the push-button deployment (or using the rsconnect interface) then you can force a new deployment by changing the document name.