This seems to be a very weird behavior.  After modifying a file,  all 
instantiated instances V of classes C in the file are no longer correct 
(i.e. instance(V,C)  returns false).   

Here's a simple example illustrating the problem  

I have a file called t1.py contains the following 
class Test(object):
    def __init__(self):
        pass


Now open sage, at the prompt do

$ sage
----------------------------------------------------------------------
| Sage Version 4.8, Release Date: 2012-01-20                         |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
sage: attach t1.py
sage: t = Test()
sage: isinstance(t,Test)
True         #### here it's correct


Now go back to the file t1.py,  make any modification ,  e.g.  enter a 
space and delete it ... save the file

sage: isinstance(t,Test)
False   ####  here it's no longer correct


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