The reply I received from my support ticket was this: "Thanks for reaching out and we apologize for this inconvenience!
Unfortunately, Roll20 has storage constraints. When a game reaches a
certain size it becomes unstable and breaks. Rather than deleting all
your content, the container it's in collapses, leaving the content
intact but disorganized. In order to prevent future breaks we
recommend deleting unused handouts and perhaps breaking the game up into
several other smaller games. You can use the Transmogrifier
(which is a benefit of your Pro membership) to easily move Pages
(including dynamic lighting), Characters, Decks, Handouts, Rollable
tables, and Jukebox playlists over to new games."