Try this.

Sub CheckedByDate3csv()
Dim ans
If ActiveSheet.CheckBoxes(Application.Caller).Value = 1 Then
    ans = MsgBox("QUESTION HERE?", vbYesNo)
    If ans = vbYes Then
 'Continue
 'enters current date and users name into selected cells
        Range("E3") = Format(Now(), "dd-mm-yy")
        Range("F3") = Application.UserName
    Else
        MsgBox ("INSTRUCTION HERE."), vbInformation
        'clears current date and users name from selected cells
        Range("E3").ClearContents
        Range("F3").ClearContents
        ActiveSheet.CheckBoxes(Application.Caller).Value = 0
    End If
End If
End Sub