The capabilities you define here are the defaults for a new installation or when creating that capability for the first time. Once a capability has been created based on this definition, changes to the defaults have no effect during an upgrade.
If you are just developing, then I would suggest that you change the live definitions in the UI at the same time as you make changes to the defaults.
If you have a live plugin where you need to make changes to a capability then you will need to write these changes in an upgrade script.
Note: Typically we do not set CAP_DENY in a capability definition, we just do not give any user the capability.
Andrew