Mill tools created in an operation will not automatically save to the library. Below are two options for saving them to a library.
Option 1:
Within toolpath parameters, right click over the tool.
Tool manager
Confirm the correct tool library is selected.
Drag the tool into the library. It will then prompt to save.
Option 2:
Toolpaths > Tool Manager
Confirm the correct tool library is selected.
Drag the tool into the library. It will then prompt to save.