Do you mean the attribute mappings between two entities?
In that case you should be able to manage them through the CRM API.
Just go to Settings -> Customization -> Customize entities -> Open one of
the involved entities -> click 1:N or N:1 relationships on the left hand side
-> Open a relationship -> click Mappings on the left hand side -> You will
now see a grid showing the attribute mappings between the two entities
involved. On the top is a Delete button.
Remark: some attribute mappings can not be removed. For example the mapping
of the id's between the two entities. There might some other system mappings
that cannot be deleted, but over all most of the mappings are editable.
Hope this helps you out.
Bertil