I am trying to clean up my long list of variables and after doing so there are several variables that show up in the drop down list when selecting in a Macro action that are not listed in Keyboard Maestro preferences under variables. Why is this and is there a way to remove those?
I am guessing that perhaps these are temporary variables that don't get saved in Keyboard Maestro Preferences.
In the image you can see when choose from a list of Variables in a macro Empty Do Not Fill, Fill With Only User Typed Input" etc.
These are called instance variables (another similar category is local variables).
Their values are set during macro running. They do not have any value when no macro using them are running. Therefore, your guess is correct. The variables in the preference are global variables.
If you have time, make sure you read the wiki page on different types of variables:
They are there when you have macros that contain these variables. If you rename those variables or delete those actions/macros, the variables will also disappear.
To find out which macros are using these variables, you may