Handles are created at runtime, hence they will differ from session to session. Use tags or names to keep your data session independent.
Retaining handlers when loading .fig file
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I save my figures as .fig, and the handlers as .mat.
When I load the .fig and .mat files, the handlers does not work. The plot that was in figure(165) does now appear in figure(1).
The .fig file contains the needed information (rename it to .mat and load it, and you will see handlers and pointers in it).
Edit: I'm currently running Matlab R2011b (7.13.0.564) and R2012b (8.0.0.783).
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