Again a feature of them switching to CGI and not staying "true" to what was previously established.
Having the nacelles glowing in Flashback is a mistake. But as for Excelsior-class engines glowing in the 24th century, I just assume they got new engines, no need to go continuity nazi on it...
but it seems odd that all of the Excelsiors we see in TNG don't have glowing engines but then as we see them in DS9 they do. So Starfleet drug their feet when it came to giving Excelsiors the new "glowing engines."
fleet shot featuring several Excelsiors (the non Ent-B variety, too) with glowing engines.
So SF took quite some time between the 2340s (when "glowing engines" started if we use the Ent-C as a guide) and the 2370s to upgrade Excelsior engines to the "glowing kind" given that all of the Excelsiors we see in TNG have dark engines and they started having glowing ones in DS9 probably around the time they went to CGI for effects.