The incubation with Proteinase K in our (extensively) tested protocol is performed simultaneously with the sample lysis (the step you mention at 70 °C for 10 min). The idea is to combine lysis and Proteinase K treatment in a single step, so to keep the protocol as short and yet as efficient as possible. Our data (and quality control) show that such treatment is very effective with relatively complex matrices, suggesting negligible denaturation with short incubation times (and enzyme excess!). With much more complex matrices like tissues, for instance, we would recommend to separate extraction/lysis step and Proteinase K treatment, and perform the latter at the optimum temperature for the enzyme 50-56 °C..