As a Roblox developer, it is currently impossible to efficiently organize LayerCollectors in folders with the “ResetOnSpawn” property disabled.
The only workaround for this problem is to not organize them at all, and parent them directly to a Player or PlayerGui instance for desired functionality.
As of right now, it seems that the a LayerCollector only checks if its a direct child of either a Player or PlayerGui instance. A desirable functionality would allow the LayerCollector to keep it’s place inside the folder it’s placed in, if that folder is also a descendant / child of either a Player or PlayerGui instance. If Roblox is able to address this issue, it would allow me to put Surface, Screen, and Billboard Guis in folders, allowing me to organize my LayerCollectors properly.