Flags once set are retained in the gedcom file permanently. They are
covered in detail in the V3 manual.
The original question covered flags set on one file not being
available in other gedcom files on the same computer.
This only effects people with multiple gedcom files and is exactly the
same as version 2's custom attributes and events, in that if a flag is
not used in a file is it not shown on the list of flags available for