SharePoint Designer error when trying to Check In a file such as CSS file: “We can’t do that for you because the file is no longer checked out or has been deleted.”

“We can’t do that for you because the file is no longer checked out or has been deleted.”
or
“Cannot perform this operation. The file is no longer checked out or has been deleted.”
It is because SharePoint Designer sometimes is out of sync with SharePoint.
Here is the Solution
Clear the cache of SharePoint Designer.

1. Close SharePoint Designer.
2. Open My Computer, paste in %APPDATA%MicrosoftWeb Server ExtensionsCache in the address bar

3. Delete everything.
4. Open My Computer, paste in %USERPROFILE%AppDataLocalMicrosoftWebsiteCache in the address bar.
5. Delete everything.
6. Open SharePoint Designer >Navigate to the “File” menu > select “Options” >click on “Application Options”In “General” tab, uncheck “Cache site data across SharePoint Designer sessions”.

Happy SharePointing !
Khojasteh (Kate)