In the MPR Supplemental Guidance ( http://www.usgbc.org/ShowFile.aspx?DocumentID=6473 ) we state:
"• Where whole project meters are cost-prohibitive or physically impractical to install
Owners of LEED project buildings or spaces that do not have meters in place that measure energy and/or water usage for the entire LEED certified gross floor area will not be expected to supply energy and/or water usage data unless and until such meters are installed. Many Commercial Interiors projects, higher education campuses, and military bases will fall into this category."
Just state the conditions you are working under in the Project Information form #1 (Under special circumstances) in LEED Online.