`isinstance` removes `cls.__dict__["__annotations__"]` in a complex setup with Protocol and ABCMeta

Bug report

Bug description:

import abc
from collections.abc import Iterator
from typing import Protocol

# ---- Expected behavior:
class Steppable(metaclass=abc.ABCMeta):
  pass

class Module:
  @classmethod
  def __init_subclass__(cls, **kwargs) -> None:
    super().__init_subclass__(**kwargs)
    name, annotation, default = "name", str | None, "abc"
    cls.__annotations__[name] = annotation
    setattr(cls, name, default)


class SequenceLayer1(Module, Steppable):
  pass


print(SequenceLayer1.__dict__.get("__annotations__"))
# {'name': str | None}
assert SequenceLayer1.__dict__.get("__annotations__") is not None


# ---- Unexpected behavior:
class CheckpointableIterator(Iterator, Protocol):
  pass

isinstance(CheckpointableIterator, Iterator)

class SequenceLayer2(Module, Steppable):
  pass

print(SequenceLayer2.__dict__.get("__annotations__"))
# None
assert SequenceLayer2.__dict__.get("__annotations__") is not None

• Failing on 3.12 and 3.13
• Passing on 3.11 and 3.14 (For 3.14 it is expected to have __dict__["__annotations__"] missing)

CPython versions tested on:

3.12

Operating systems tested on:

Linux

Run the reproducer involving Module.init_subclass, CheckpointableIterator, Protocol, ABCMeta, and isinstance on Python 3.12 and 3.13, then compare it with 3.11 and 3.14. Trace how SequenceLayer1 and SequenceLayer2 receive annotations and identify where the second class loses its entry. Done means the behavior is explained and a regression test covers the affected version range.