The following forum message was posted by jaygengelbach at 
http://sourceforge.net/projects/pydev/forums/forum/293649/topic/3843753:

Okay, played around with this for a while, and made a little bit of progress.

Deleting the file doesn't seem to have any effect.  I copied the whole
google_appengine directory to another directory, then changed the project to
point to that one instead.  After a restart and force rebuild, it had the 
correct
data from the file system.  Then I made an edit on the file system, 
rebuilt/restarted
again, and the change I made was reflected in Eclipse.

Here's where it got interesting.  I kept having to run the editor in admin mode
to have permission to modify the file.  I thought the permissions might have
something to do with the problem.  I modified the file to give me full access
to the file.  After doing that, I was able to modify the file in Eclipse, and
the edit showed up on the file system.  Then I tried reducing the permissions
again, and making an edit in Eclipse.  That edit wasn't reflected on the file
system, as you might expect.  However, after performing that save in Eclipse,
the link to the file system got irreparably broken.  Edits in the file system
don't show up in Eclipse, and saves in Eclipse don't show up on the file 
system--even
if I tweak the permissions again.

I'm not sure how I would have broken the link in the first place.  But I'm 
guessing
that if I try to save to a file I don't have permissions to modify, pydev or
Eclipse creates its own copy somewhere, and starts to use that.

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