I personally migrated all my workspaces by recreating them from the new UI (make sure all of them are public and have a “module” selected) - since it was too much of a hassle to manually change the JSON files to support the new format.
So you mentioned that you have a custom app that you developed.
In this case, on your local machine (which would have developer mode enabled), you can create a new Workspace from the main page. You need to click on the Workspace button in the top right (beside “Edit”). Create a new “public” workspace.
Then, to ensure that your Workspace is added into your codebase, you need to go to the Workspace List, open the Workspace Form and then link it with any module
This step would add the Workspace JSON file to your codebase, which you can then push to your remote repository. On your production system, you would simply run bench update to pull all changes and build the new workspace.
I managed to solve the above stated problem. What I did was click on the edit button of each row that was giving error and then just tweaked the Label.