Flags are available at the dump level in the IPB, as they are recorded on the second basis by the online system. In the hpb file, they are stored in the data modified section, and only one value per observation is kept. In the case when one uses an hpb file, the actual flag will be a logical .or. of the IPB and hpb flags.
An option exists to store the flags only in memory if they are to be reset after some operation, as it is much more efficient. Command MASK allows to mask a given flag, while command MARK can be used to set a given flag (for all observations, contrary to the STORE FLAG /MEMORY option that works on the current index).