Why are you waiting for your new WP before applying PR. This is what you can do but it's up to you. If you are ready to send your PR application, you can write something like" I have already requested restoration of my status and paid a $200 restoration fee.” Then, depending on how cautious you want to be, you can either
1) pay the $200 fee again (to avoid CIC asking for it, which might cause
delays and complications on your wP) include that receipt and
write “I have included an additional restoration fee with this new application just in case, but I would like to request a refund of the restoration fee payment that CIC does not use”
or
2) you can just include a copy of the restoration fee receipt that you used
on your WP application and write “I have included a copy of the receipt that I used to pay the $200 restoration fee on my WP application.
1) pay the $200 fee again (to avoid CIC asking for it, which might cause
delays and complications on your wP) include that receipt and
write “I have included an additional restoration fee with this new application just in case, but I would like to request a refund of the restoration fee payment that CIC does not use”
or
2) you can just include a copy of the restoration fee receipt that you used
on your WP application and write “I have included a copy of the receipt that I used to pay the $200 restoration fee on my WP application.