You should check if there is a hidden file for that. Many applications like Word, Vim create a hidden file that show that the file has been opened by the app. Deleting this file might get rid of this problem.
On 'My Files' app settings you can set to show hidden files and check if there is a file with similar name that begins with a dot '.'. e.g. the file is called 'myNote.txt' and the hidden file is usually called '.myNote.txt'
