Please note that manual availability option was made basically for the properties which want to use only the Channel Manager package and they don't have access to the BedView so they have to control the availability manually.
If you set up your availability manually in Availability and Rate Calendar it will have the red color. The auto availability will have black numbers.
In order to restore the auto availability choose the date or dates you want to apply the changes for and right click on them.
Choose the Restore Availability option.
The numbers will turn black again.