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It seems that notepad.getCurrentDocIndex(view) assumes view is always equal to 0 (the left editor) even when passing 1.
Don't know if it's a bug of the Python Script plugin or of Notepad++ itself.
I tried to use Python Script to make a "work-around" for Compare Plugin losing highlighting (check http://stackoverflow.com/questions/14799891). But it seems that happens what azrafe7 said with previous post. So my script works only if the two files compared have the same positions in the two views.
Confirmed. This is actually already fixed in the source for PythonScript. As there's a few fixes, I'm going to try to release a new version shortly - nothing big, just the few fixes that have been reported.