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

I believe the problem is that there are paths still pointing to the old 
version...
Please recheck the values you have at the project properties (right click 
project
> properties) > Pydev - PYTHONPATH > source folders, external source folders
and string substitution variables (especially the string substitution
variables).

If they are all correct, please check if you added a path to the old app engine
in your interpreter configuration (window > preferences > pydev > interpreter
- python).

If it still seems all correct, please report back.

Cheers,

Fabio

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