package.py package or
package.py all and the command
unity.py prepare can lead to errors when using Unity Pro. In some earlier versions of Unity, running batch mode would delete the Pro license. The same issue didn’t exist when using the Personal license.
As a workaround, re-enter your license number and run the command again. Note that the license will get deleted every time the batch mode is called (when using the Python script related to Unity).
To solve the issue, update to a newer version of Unity where this issue doesn’t occur.