Place lima beans in large bowl with enough water to cover by 5 inches. Soak overnight.
Bring 2 cups water and dried mushrooms to boil in small saucepan. Using slotted spoon, transfer mushrooms to medium bowl; reserve liquid in saucepan.
Heat oil in heavy large pot over medium heat. Add onion and garlic; sauté until onion is tender, 10 minutes. Drain beans; add to pot. Pour in mushroom liquid, leaving sediment behind. Add 6 cups water. Bring to simmer; skim foam from top. Stir in red pepper and thyme. Simmer partially covered until beans are tender, 45 minutes. Season with salt. Chop mushrooms; add to pot. Simmer uncovered over medium heat until beans and mushrooms are very tender, stirring occasionally and adding water to thin as needed, about 15 minutes longer. DO AHEAD: Can be made 3 days ahead. Cool, then cover and chill. Rewarm beans before continuing.
Add chard to beans. Cover pot; cook until chard is tender, stirring often, about 8 minutes. Season with salt and pepper.
