Short Answer
Deteriorated decking may not provide an appropriate substrate for the new roofing system. Replacement of damaged decking may therefore be necessary.
Detailed Explanation
Rotten decking can't properly hold the fasteners that secure the roofing system. Shingles nailed into soft, rotted wood can blow off in wind because the fasteners pull out. Underlayment and ice and water shield won't adhere properly to deteriorated surfaces. The structural integrity of the roof may be compromised, leading to sagging or even failure under snow or wind loads. For all these reasons, rotted decking must be replaced before the new roofing system is installed. The good news is that decking damage is usually localized — it's rare for an entire roof deck to need replacement. The bad news is that the full extent of damage often can't be seen until the old roofing is removed.
Why It Matters
Installing a new roof over rotten decking wastes the investment because the roof won't perform properly and may fail prematurely.
When Repair Makes Sense
Decking damage is localized to specific areas and the surrounding deck is sound.
When Replacement Makes Sense
Decking damage is widespread, indicating long-term moisture problems that may have affected structural members as well.