Whether an instrument and/or flight guidance system will indicate the GS deviation or not, depends on how the instrument or flight guidance system is programed to use the ‘flag’ signal. Deviation and flag are usually separate signals from the receiver. It may also depend on the receiver type, digital vs analogue.
Many EFIS will not show a deviation with a flag, some remove the GS scale – perhaps the E190; perhaps other older instruments might show a (incorrect) deviation, or even not flag the signal at all; beware.
Such situations require pilot evaluation, an awareness of altitude vs range from the runway, vertical speed, aircraft configuration, etc.
Crosscheck approaches with several sources of information.