So, you’re in SharePoint Designer 2010 and you get this error that says it can’t perform the operation when you’re trying to check in your changes. Also, it tells you that the file is already checked in or it has been deleted. You’ve scoured the internet, deleting all the cache files you can find, trying every little thing Google has found for you and you’re at the end of your rope, because, so far, nothing has worked for you. Have no fear, the answer to your problem is near, with a solution that, at least, worked for me.
I opened the file from SP Designer 2010 and copied the entire contents to the clipboard, pasting all the text into a NotePad file. Next, I deleted the file which was giving me all the problems.
Once that was done, I created a new file (.aspx) in the same library/folder, using the old file name. Once it was created, I removed the initial content and pasted in all the text from the NotePad file. All that was left was saving and checking in (which worked).
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