The words except as or except that indicate an exception to the rule in connection with which it is given. If an exception is specific, the agreement should likely address what happens (or who should do what) in connection with each such exception.
The relation between two or more contract provisions is often expressed by starting one of the provisions by:
Except as otherwise agreed…
Except as otherwise specified in a Purchase Order…
Note the subtle difference between the two above examples, which is the limitation to where such deviating agreement can be made. It may well have little meaning but is sometimes useful. For example, if in a framework agreement another provision requires that all deviations from that framework agreement are invalid unless such deviating provision explicitly states that it is intended as a deviation and from which provision it deviates.
The words except as otherwise agreed are sometimes inserted to invite the reader (at a later stage) to consider proposing a deviation from the provision. This is because many people are psychologically inclined to believe that they are bound by the contract text (whereas the literal text may well imply a flexibility that is not at first present in the words). For example, many contractual prohibitions or restrictions are not per se carved in stone but require a proper explanation before a party would waive a violation in a certain context.
Best practice – be specific. Rather than the abstract phrase except as otherwise agreed, it is recommended to be specific and identify which clause actually does limit or qualify that provision.
Other qualifiers or subordinations. The counterpart of except as otherwise agreed would be notwithstanding anything [in this agreement] to the contrary. Obviously, this counterpart clause means that the provision at hand may well limit or qualify another provision (of the contract or elsewhere). Whilst these clauses imply a rule with specified exceptions, the phrase subject to introduces a hierarchical priority of clauses.