This work explores the challenges of using life cycle assessment (LCA) and life cycle cost (LCC) analysis to provide easily accessible decision support for early product development in cases where intellectual property (IP) and privacy issues require special consideration. Innovation research projects with partners representing different links along the value chain are potential examples of such cases. A case study in which spreadsheet-based cradle to compounder's gate LCA and LCC screening tools were created for candidate flame retarded polymer formulations exemplifies the need for better solutions to overcome problems associated with lack of transparency due to IP/privacy concerns. These problems affect data quality, scaling up processes, and uncertainty of the results. The consortium in this case study had a common overall goal, although each of the partners had a unique perspective on the polymer development process and different IP/privacy needs. The measures used to overcome the challenges include aggregation, normalisation, and omission of costs and impacts common to all candidate compounds. The resulting LCA and LCC screening tools represent a compromise between providing the requested information at the level of detail required by the partners and reporting results that are as accurate and useful as possible. The findings are: in cases where absolute secrecy must be maintained, no one can learn which materials and processes provide the optimal results; appointing a trusted third party to handle sensitive inventory data can cause increased uncertainty of the results due to lack of peer review; the results of the work cannot be built upon by subsequent research.