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I think, I came across a bug in SQL Developer:
SQL Developer version: 3.0.04
create table USER_A.foo (val NUMBER not null, CHECK (val IN (1,2,3)));
create table USER_B.foo (val NUMBER not null);
Comparing these two schemas does not give any difference. However, when not null constraints are removed from both tables, then check constraint difference is correctly reported.
Does not reproduce in SQL Dev 4. Seems like the comparison mechanism was changed, so can close the topic