While you were working with SharePoint designer 2013 you might face a situation where you will popup with an error “The file is no longer checked out or has been deleted” at a time when you try to check in any of the file from SharePoint designer. I tried restarting the SharePoint designer, resetting the IIS and restarting the machine even.
Finally it seems that need to clear the cache in local app storage to resolve the above error.
Navigate to your local app settings cache folder located in the below location and delete the files corresponding to your site.
For ex: C:\Users\Ammar\AppData\Local\Microsoft\WebsiteCache (my local machine path)
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