What is a flagged medical chart?

"Flagged" just means the chart has been identified as needing special attention for some reason.

Examples:

If a hospital was doing chart reviews they may "flag" all of the charts of people seen on a given day, by a certain doctor, or with a certain diagnosis.

If there is an adverse outcome or patient complaint they may "flag" the chart for quality review.

If the doc wants to give a certain vaccine but runs out (s)he may "flag" the charts of the people seen while out to be called back when it is in.