Python 3.5.2 (and Python 2.7.12) uses Py_TPFLAGS_IS_ABSTRACT while PEP 3119 menttions "Py_TPFLAGS_ABSTRACT" for it. At some point had the name of the flag been changed without modifying PEP?

Probably.  PEPs, once completed (unless they are informational PEPs), are historical documents, and the real implementation may diverge from the PEP immediately, or after maintenance updates.  The real documentation for the added feature should be in the main docs.  We are not always good about making that true, and we do reference the PEPs, and so sometimes we do update them.  I'll leave this open so someone knowledgeable about it can decide if this should be fixed, or if there are missing "real docs" (I don't get hits for either constant grepping the docs).

Presumably when the implementation was done the IS_ABSTRACT name sounded more logical than just ABSTRACT. Since the PEP doesn't *specify* the name of this flag[1] I see no reason to change anything. Closing.

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[1] The PEP mentions this flag exactly once:

    (If this were implemented in CPython, an internal flag
    ``Py_TPFLAGS_ABSTRACT`` could be used to speed up this check [6]_.)