Single partition layout (one big home) may not be ideal when flashing new firmware. Since /home/opt is extension of root file system (most installed 3rd party packages has most bits there) and reflash clears package database I wouldn't be surprised if some initial setup after firmware reflash would do mke2fs on whole home partition to clean leftovers of previous system. Having separate data partition for /home/user/MyDocs might be handy then.

BTW, currently it is not doing it but to me it looks more like bug than intention.