The documentation on the wiki needs to be updated to accurately reflect the usage of flags and how they need to be defined in the metadataxml in order to use them in a query. Here is a brief explanation of there usage:

The <Flagstouse> tag determines what flags can be used when defining a value constraint in the query tool views. If there are no values defined at <Flagstouse> tag then the option to constrain a query by the flag will not appear in the value constraint window.

Examples:

The searchable flag for a microbiology test would most likely be Abnormal and in this instance the metadata would be <Flagstouse>A</Flagstouse>
The searchable flag for a numerical lab test like Potassium would be High or Low and in this instance the metadata would be <Flagstouse>HL</Flagstouse>