Lost desktop files

When we closed out an imaging program, we noted that all the files and folders on the desktop were gone. just the Hard drive icon was there. There was maybe 15 folder with several GB total on the desktop. But the desktop was clean. The trash still had a lot of old files/folders, but nothing from the desktop was in the trash. This is very serious, and I'm wondering if anyone knows how a iMac could selectively delete so many files, w/o emptying the trash.
Thanks.
-wayne

When we closed out an imaging program...
What does that mean? Does it mean that you quit the program? What program was it?

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