I use Xplorer2 by zabkat. I use the Pro version, but there is a free Lite version as well.
It is a Windows Explorer replacement that provides dual panes for file management and many other advanced features that are incredibly useful but not found in Windows Explorer.
In the case of your question, the Pro version provides a feature called a scrap container.
Manage files from many folders at once
xplorer² has a special kind of window called scrap container where you can place files from many folders and deal with them all at once — like the find files result list, except that you control what goes in (aka virtual folders or playlists). You can save and reload scrap lists, organizing your content regardless of its physical location. You can even browse folders flat, recursively including all their subfolders!
This feature is not available in the free version.
You drag and drop any collection of files and folders into the scrap. Then highlight everything in the scrap, drag and drop onto the web page. I have used this mostly with Google Drive. Works very smoothly.
I have been using dual pane file management since DOS, so I can't live without it. You may only use xplorer2 for this one purpose, or do I like I do and set xplorer2 to completely replace Windows Explorer.