> is sub-folder mode broken in ClrMame Pro 3.65b?
> A generated dat (like below) with 3.65b would delete
> all dirs in each zipfile.


Works fine here.
Don't mix directory entries in zipfiles with zipfile-folder-structs. Sometimes zipfiles got a subfolder entries which is just a dummy entry which can be removed since each and every file is stored with the full path information. ClrMamePro lists such dummy entries as
"unneeded folder:". You can enabled/disable this behaviour in settings->zipoptions->mark useless zip structs as unneeded.

Roman Scherzer
ClrMamePro