Thanks for your reply -
Hmm, maybe that is the intention, a possible explanation.
Although, I would argue that it is not a software’s prerogative to disallow users to leverage certain file types. There might be a few regular file types that cannot be opened on a Mac or vice versa for Windows. It does not seem that Endnote filters any such file types.
I suspect that the actual reason is that bundles can be very elaborate with many contained subfolders and files. Programming to (recursively) upload bundles and somehow make them presentable online would be quite a task.
(To give some background: I am trying to make “Skim” work as my PDF editor with Endnote. So far, I have not found any constellations that works, despite that Skim allows many ways to store edited PDFs: bundles, notes file separate from PDF, extended file attributes, etc. None of these work right for Endnote attachments. A pity. Saving flattened annotated PDFs would defy the purpose of using Skim. But this topic belongs in a separate thread…)