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Thank you for making your source files available to us. It's nice to be able to learn from other people's projects!
As for your question about the scene editor : I have only been using WME for a few weeks, but one thing that comes to mind is : have you been changing your directory structure at all ? I mean, moving folders around and such ? Once I point to the image/sprite again in the editor, it doesn't disappear on closing & reopening the editor... So, all seems to be fine...
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