Hi Kiyoshi,
There was no release 2.2.3.8, its 2.2.3.3.
I did not think folder based sub sites was even working on Mono.
If you had it working and there were 2 sites there would be a folder Data/Sites/2, did you delete this folder? The upgrade process would not have touched it so if its gone it got deleted by someone, hope you have a backup and can restore it.
Joe