I don't know which of the many attributes you have used to make /var/shares a 'readonly' share, and I don't know which sharing protocols you are using at all. So I can only vagely guess what happened.
First of all, I would think the management framework would never recursively apply attributes to existing directories or files. And on the share level, the management framework won't adjust settings of other shares even if their paths overlap. So I'd suppose the settings you made for the other shares are not lost or overwritten by anything.
If you have set the permissions for the share's root directory (removed write or access permissions) then this could affect the accessibility of the directories inside. Just set the permissions back, this can help. For making a share read-only, better uncheck the 'write acces for the XXX protocol' permissions at the share level; this should not interfere with other shares.
If it's not about the pure directory permissions, please tell something more about the way you have created the 'backup' share, and be a little more specific about the errors you're seeing.