When outputs are removed, we currently lose all window state. In certain cases where the output is disabled rather than removed (such as a laptop lid closing or switching to a different TTY), it would be much better to keep the frame tree so that you don't have to reorganize your windows every time you close your laptop lid.
There are disabled flags in wlroots, but I'm not sure how they work or how disabling relates to destroying, so much more research is needed.