We faced the same problem as we realized that the Upload control for Domino 12.0.2 still would only upload on file.

On OpenNTF there's a project YouAtNotes HTML5 Multi File Upload control that showed us a way to solve our problem. In short: as the Upload control renders as standard HTML <input type="file"> the OpenNTF solution uses a hidden upload control and some JavaScript code to iterate through all files and do a XHR post request for each of these files.

Probably the OpenNTF project can guide you to a solution, too.