It depends if the timber substrate is sound. If there has been a long term leak, or the decking is chipboard, then the roof may need reboarding in places. If the substrate is sound and the felt cleaned of dust etc then the EPDM can probably be adhered directly to it using contact adhesive (although this is more tricky to install).
To save the time and expense, some customers simply overboard their roofs with new ply or OSB, screwing into the existing substrate.