After a longish layoff of a couple of months due to a very sore and stiff knee, I started back on the programme a few weeks ago - dropping back in at Week 6. It's been really good - I hadn't really lost any stamina and the knee has been behaving itself, as I went through Weeks 6 & 7 (again) and now Week 8 (for the first time) without too much trouble.
Just have Week 9 ahead of me now!
The rest/break did me a lot of good, so if you are feeling pain, ease back and take it easy for a time - you can always come back when things ease