FFVI: Divergent Paths

@PowerPanda
Just reminding you about that Kefka's Tower critical bug to be fixed for 1.2!

Thankee!

Question: Even though the sparkling red isn't there, did you attempt to check the chest anyway? Because the red sparkle is an NPC while the actual activation of the chest is event-related. I'm just curious if the event part of it was broken as well, which may or may not help resolve this.
Also, which way did you exit the tower, by going all the way back to the start and using the crane/grapple hook, or by casting Warp?

EDIT: After re-reading your initial post about this, I'm gonna guess you made it all the way up to defeating the 3 statues, and then warped out? I just tested that, and yes, the red sparkle NPC is no longer there, but searching the chest (from either the bottom or the right side) still activated that event that clears the rubble/builds the stairs to move up... SO, I'm gonna guess that you did not try and re-check the chest assuming that since the red sparkle is gone, it wouldn't work. It should definitely still work though. This is the same in vanilla. I guess that red sparkle NPC spot gets erased so that other NPC on the map can be shown, or it's simply an oversight.