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I'm not familiar with this problem (I only keep one or two apps on the card)... I've never had a shortcut completely delete itself. Odd.
So I'm not sure about recovering them, but you don't need to re-install just to create new shortcuts. Just use File Explorer to navigate to the exe, tap and hold with the stylus and choose "Copy".
Then go into \Windows\Start Menu\Programs, tap and hold on a white space and choose "Paste Shortcut". Note this is different than doing a Paste (which would copy the entire program into that folder. "Paste Shortcut" does exactly what it sounds like.
Anyway, my guess is that some program you ran (memmaid?) saw those shortcuts as orphans because your SD card wasn't in the slot and deleted them for you. I have never seen Windows Mobile delete shortcuts on its own.
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