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I had a VM that no longer exists, and neither does its VDI file or snapshots folder (long story), but the VDI file still appears in the Virtual Media Manager (with yellow warning triangle).

How can I remove it?

Edit: Thanks for the suggestion, but it doesn't let me remove it, presumably because of the snapshots (and it won't let me remove those either), and the Release option is greyed out:

Virtual Media Manager screenshot

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You'll have to "release", then "refresh", then "remove" the VDI file in the Virtual Media Manager. It might give a warning but it should work for you.

enter image description here

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