SharePoint Designer sometimes is out of sync with SharePoint. SharePoint Designer will incorrectly show items as checked out (or checked in) and refuses to be update with the actual status. In some cases the following error will be shown when trying to check out/in an item.

“Cannot perform this operation. The file is no longer checked out or has been deleted.”

Solution
The solution to this problem is to clear the cache of SharePoint Designer.

1. If opened close SharePoint Designer
2. Open the folder %APPDATA%MicrosoftWeb Server ExtensionsCache
3. Delete the contents
4. Open the folder %USERPROFILE%AppDataLocalMicrosoftWebsiteCache
5. Delete the contents
6. Problem solved.