We had a requirement to deactivate/disable an APEX application but retain (not delete) the definition from developer console. This was so that users can start using another brand new application as a replacement to this old app and just so that they don't accidentally access the old app from bookmarks etc.
We can manually disable an application via
Shared Components -> Application Definition Attributes -> Availability -> Status
Set Status to Unavailable
And you can set the appropriate message to be shown in "Message for unavailable application" field -
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