You can do this by hand or in a script.
Use Replace Field contents with the calculation option and you can clear any field for all the records in your found set in a single step. Use "" as the calculation expression to clear the field.
Ok, and what about the opposite - for a "Check all Checkboxes" script?
Use this as the calculation's expression:
ValueListItems ( get ( FileName ) ; "valuelistNameInQuotes" )
You can use that inside a set field instruction to click all check boxes for a single record or inside a Replace Field Contents to do it for all records in your current found set.
Note: You could also use valueListItems ( "NameOfYourFileInQuotes" ; "valuelistNameInQuotes" ) , but then this would fail to work correctly should you ever rename your database file. Get ( FileName ) avoids that issue for you.