Sorry to hear about your deleted PDF file. To delete a sticky note, use the “Delete Annotation” option. Using the command “Remove” deletes the PDF file.*
Unfortunately, Endnote does not have an “undo” feature which you might submit as a suggestion on the Product Suggestions section of the forum. There are software applications to recover deleted files but it will take time on your part to locate and try out the software which may have varying degrees of success. You may also risk exposing your computer to viruses or malware if the software is from an unknown or questionable source. Recovering your PDF may also not include the changes you made as it seems like the PDF was deleted before it was saved.
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*Note to developers : It might be helpful for users if the “Remove” command is relabeled to “Delete File” and also enable deleted files to go into either the Endnote Trash bin or the computer’s Recycle bin which would allow for recovery.