Hi,
For your issue, try clear a cache in the local app storage.
Navigate to your local app settings WebSiteCache folder: C:\Users\admin\AppData\Local\Microsoft\WebsiteCache,
delete all the files or just the ones that correspond to your SharePoint site. When you restart SPD you may have to check in/out the files.
Also, it is possible that the file might not actually be checked out or not exist on the server.
If you want to ensure that the files you want to check in still exist on the server or been checked out, initiate a manual synchronization before attempting the check in.
Besides, Here are some similar issues, you can take a look at:
http://passionatetechie.blogspot.com/2012/03/spd-workflow-error-solved-cannot.html
Lisa Chen