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In my case it wasn't the boot entry being removed. It actually ate the partition. When installing Linux Mint, I resized the Windows partition in Linux. Then I noticed that Windows absolutely didn't recognize that change, and thought its partition is still as big as it used to. Then on a restart it hit me with the "Repairing drive C:" which killed the Linux partition leaving just something corrupted.
"Repairing"Windows: "Let me repair Linux for you"
Ew, you've got a linux on your windshield, lemme just hit the wipers for you real quick
Have you tried first resizing the windows partition inside windows? That's what I did and my dual boot has stayed intact
Yep, that's what I did later and it worked.
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