Keith- Beings that this project is still in the prelim stage, I would post this same question on the Pond Boss Forum - http://forums.pondboss.com/
. I think you will find that you will get an answer similar to mine.
Although Larry is correct that a biofilm will form on the liner if left exposed to just the pond water, this will in no way come close to duplicating the existing benthic layer that can be reused. A biofilm is just that and does not provide a habitat for micro- and macro-invertebrates (annelids, arthropods, insect larvae etc.) that a true benthic layer will. These organisms are all an integral part of the food web and carbon cycle. Even on new earthen pond contruction where a liner is required because of existing soil conditions, a layer of soil over the liner is recommended. The fact that you will have this substrate already available, it seems foolish and counterproductive not to reuse it.