Hmm, I don't think there is a bulk delete function for mobile bookmarks. However, is it really necessary?

If your concern is mixing bookmarks together between desktop and mobile, that shouldn't be an issue. Your mobile bookmarks are kept in a separate category (Mobile) from the three used on desktop (Toolbar, Menu, Other) so you can ignore them most of them time but find them in the Bookmarks Sidebar when needed (below the three desktop categories).

Or maybe there is a different reason...

I do not what what is on the phone to be synced. I think by mistake I might of synced it and may have to reset my password again. been a long haul on this.

from what I have seen the sync populates the regular bookmarks/other bookmarks/bookmarks toolbar. I have nothing in mobile bookmarks.

not sure if okay to just delete the folders completely, or if and uninstall would start fresh.

If you want to freshen your mobile installation, I think going into Android settings > Apps and clearing data would flush it. But for just desktop bookmarks, it's probably more efficient to remove them on desktop??