Uploading PDF attachments to EN cloud when "copy new file" is unchecked

I unchecked “copy new file” to handle PDFs in a way I prefer. However, when I sync my desktop EN with the EN online space, it seems that attachments won’t be uploaded… Do I need to do it manually?

It was my understanding that the files need to be in the relative folder location (copied) for the auto functions like “compress library” and syncing to EndNote Online to work on the PDFs.  There is a way to retroactively copy them all to the relative location (on a PC: References menu>file attachments>convert to relative links) if you should decide you want to use these functionalities.  


The problem with “relative folder” approach is that it will end up with dozen of randomly numbered folders, which some people may not be happy with that.

Maybe it’s easier to save my PDFs in Dropbox, and then store the absolute links in my EN