Flags are discussed in detail in the CLIC manual. Remember the differences between a Flag (permanent problem indicator), a Mask (temporarily ignore some flags), and a Mark (temporarily set some flags). The STORE FLAG command is the preferred way to flag data. The index must have been defined before. The FLAG and UPDATE commands are only used in case of record based flagging.
If a whole scan is bad for all correlator subbands and all baselines, it is easier to tag it using command TAG with a poor quality indicator. The scan will then be totally ignored if an appropriate quality level is specified with the SET QUALITY command.
As for scan selection, we highly recommend you keep an accurate log of the flagging in a .CLIC procedure.