I'm using the default template with square thumbnails so I'm using a lot of custom crops. I temporarily tried out another template and all of the custom crops disappeared once I switched back to the default template (which makes sense now that I think about it).
Are the custom crops saved in the database? I have a backup of the database made after the last time I uploaded photos. If I restore the database using the September 20th backup, will the template, custom crops, and all images be back the way they were that day?
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Restoring the database to a particular date will indeed restore the croppings in effect at that date. We will presume that you were running the same version of Zenphoto on the 20th as you are now, though.