I just thought of something horrific!
Every time a route ends in this thing, the character either is still there on reset to common, or is obliterated. IF the character is obliterated, they are gone in the next go through and if they are still there you can’t do that route again.
Check it: When you complete a route and a character and Otonashi get all romance-y, and perhaps this could be some retconning OR just a better detailing of this dynamic that we don’t fully understand, love happens and the shadow program begins that wipes everyone out and restarts the world in a way that that doesn’t happen again. If a character is obliterated in this process, however, the program still activates- but doesn’t catch the character that is no longer in the world so they are then gone and forgotten in the next go through.
Just a basis of some theorizing on this games format.
The weak joints are non-romantic routes, of course, and what else would trigger the program.