Hi Chris,
there is a way utilizing SQL for that.

Run the following SQL Code on your Portal:

SELECT [TabID],[PortalID],[TabName],[TabPath],[SkinSrc],[ContainerSrc]
  FROM {databaseOwner}{objectQualifier}Tabs
  WHERE [SkinSrc] IS NOT NULL

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Herzliche Grüße aus Hückelhoven
Frank Wahl
www.eagleworx.net

I love coming across old posts that solve my issues! However, I had to modify your SQL just a bit in order to also check for containers that are in use:

SELECT [TabID],[PortalID],[TabName],[TabPath],[SkinSrc],[ContainerSrc]
FROM {databaseOwner}{objectQualifier}Tabs
WHERE [SkinSrc] is not null or [ContainerSrc] is not null

Having done that, and using DNN 07.00.06, when I go to the Admin / Skins page, the Aphelia skin and containers still say that they are in use even though the above query returns no results. Any ideas?

PS - Request to DNN Core team: Include a utility on the skin page to deactivate and delete (or uninstall) a skin, replacing every instance of that skin with another (that the user has selected).