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Alternatively, change the representation of flag values from integers to some class extension that supports the common bitwise operators.
As a very rough sketch:
>>> class FlagInt(int):
... def __or__(self, other):
... return FlagInt(int(self) | int(other))
... 
>>> f1 = FlagInt(1)
>>> f2 = FlagInt(2)
>>> f1 | f2
3
>>> isinstance(3, FlagInt)
False
>>> isinstance(f1 | f2, FlagInt)
True
That way, flag arguments can be determined at runtime to have derived from the proper flag values.
This kind of approach may have some backwards-incompatibility, unfortunately, since other folks have been hardcoding integers rather than use the flag constants. Other concerns might include serialization, in case someone tries to save a FlagInt somewhere and pull it out at some other time.