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When a class definition was re-executed (reload, exec ..) , pickling of existing instances fails for to picky reason (class object id mismatch). Solved by the one liner patch below.
Rational: Python is dynamic. Like with any normal attribute lookup: When its the same module/..name this class is really meant - no matter about its id. 
(During unpickling its another id anyway, the code may have evolved years ...)
diff -ur --strip _orig/pickle.py ./pickle.py
--- _orig/pickle.py	2008年09月08日 10:58:32 +0000
+++ ./pickle.py	2011年11月24日 15:47:11 +0000
@@ -747,7 +747,7 @@
 "Can't pickle %r: it's not found as %s.%s" %
 (obj, module, name))
 else:
- if klass is not obj:
+ if klass.__name__ != obj.__name__:
 raise PicklingError(
 "Can't pickle %r: it's not the same object as %s.%s" %
 (obj, module, name))

Hm, this change allows many other *undesirable* objects pass the test as well. I'd prefer to stick to the rule, "when in doubt, raise an error".
Maybe using == instead of 'is' as the test would be acceptable?

Well, "==" whould allow the wanted feature by exception through meta classes for concerned classes:
>>> class X:
... 	a=1
... 
>>> Y=X
>>> class X:
... 	a=1
... 
>>> Y==X
False
>>> class XCompare(type):
... 	def __eq__(self, other):
... 		print "tolerant class __eq__"
... 		return self.__name__ == other.__name__
... 
>>> class X:
... 	__metaclass__ = XCompare
... 	a=1
... 
>>> Y=X
>>> class X:
... 	a=1
... 
>>> Y==X
tolerant class __eq__
True
>>> 
Better than nothing. Its a improvement generally, independently.
But thinking about my acutal use cases and all: It still doesn't satisfy. I don't want to introduce this extra magic on all those classes just for that feature - because when needed, the majority of classes are concerned (see below). One can have only one meta class ... its too tricky and off-road to guess for most programmers ... 
"when in doubt, raise an error": That is IMHO too rigid here, and generally when a feature is then hindered too much. Aren't warnings the right tool for such case? If really rarely there is problem, should it surface easily already during dev & test time?
Compared to the everday life danger of Pythons dynamic attribute access, version incompatibilities, etc. its about a rather harmless issue here.
Now I'd vote for a warnings.warn upon "==" (or old "is") failing , and then an error only when the .__name__ is not matching too. A warning at dev & test time should be enough, when just "==" (or "is") fails. 
I mainly like the tolerance during development: e.g. fast reload style edit-run cycles (reload sometimes improved with special reload fix code), because I noticed that 95% of code changes/bug fixes do not require a full expensive app-restart. This pays off particularly with bigger GUI app development/fixing and similar, where lot of status is accumulated expensively during run time.
But I wished that feature already for a deployed app too.

What you're seeing here is just one of may things that go subtly wrong when you reload a class. I don't think we should fix this one aspect while leaving so many other bugs due to the same root cause.
It would be better to focus your energy on a way to improve reloading, e.g. make it so that the identity of global functions and classes doesn't change when their module is reloaded. (You'll find it a tough problem, but note that it's been solved for at least one specific instance: modules *do* retain their identity, so maybe you can use that as a model.)