I am not sure that I fully understand your question, but I think that I do.
If I am off base please excuse me, I just want to try to assist you.
Anyway, if the grade is changing and all your other timbers are level with the ground, then you are going to have to do some doubling up and walk the timbers up the grade so you have a border for the pavers.
Your timbers will essentially look like stair risers traversing up the hill. you will have some fill in to do and you should be sure to make sure that the new earth is tamped and watered down so that you have a solid subbase for your pavers. I would use all sand for this situation since it is molecularly tighter and will compact better and tighter. Water frequently to aid in the compression.