In regard to - “Is there any limitation on the length of the name of the PDF file?” - EndNote does not have its own specific limit. However, the Windows operating system typically imposes a limit to the overall length of a file “path” to a maximum of 244-260 characters - depending on the exact conditions/version of the operating system. EndNote’s attached files are impacted by this Windows limitation as are nearly all other files used on a Windows-based computer.
I would recommend moving the PDF / or the EndNote library (including .data folder) in question to a location that is not deeply nested in a set of folders and see if this resolves the issue.