Salesforce users are granted access to Custom Applications by profiles. If the user is assigned a profile that is selected for an application, then the user can access the application.
If a Custom Application's profile assignment has changed, you can use Gearset to migrate the changes to another org or source control system.
Deploying permission changes
Run a comparison with the Custom application and Profile metadata types included in your metadata filter. If your Custom Application is part of a managed package, you will also need to select All on Include managed packages in the metadata filter.
The comparison results will show the individual changes under the Profile: Application visibility metadata type.
Note that because Gearset shows metadata in its constituent components, the Profile and the Custom application will not show any differences themselves, while the Profile: Application visibility will show up as Different.
You can then deploy this specific change without fear of overwriting other changes associated with the wider profile.
Deploying application permissions for permission sets
App permissions for permission sets appear to be not supported by the metadata API. Because of this, any changes to app permissions for permission sets will need to be set manually in the target org.
Still stuck?
If you are having any problems with deploying Custom App permissions, just let us know.