IterateOverAllEntriesAndPerformTask

tell application "TaskPaper"
    tell front document
        repeat with each in entries
            -- perform task
        end repeat
    end tell
end tell

For example to remove the @today tag from all entries that have the @done tag you could use this script:

tell application "TaskPaper"
    tell front document
        repeat with each in entries
            tell each
                if (exists tag named "today") and (exists tag named "done") then
                    delete tag named "today"
                end if
            end tell
        end repeat
    end tell
end tell