Denial of EA PR2

A client has asked for my advice in appealing the denial of PR2. I've taken a quick look at the review comments but will be digging deeper into it in the next couple of days. They are the developers of the building and they did the LEED documentation themselves. This is a mixed use office/warehouse building, approx. 90K SF with more SF in warehouse than office. Under EA PR2, they chose Option 3. The reviewer(s) listed 8 items that would need to be fixed, then item #9 which stated that their project was not eligible for Option 3. They were advised to appeal and submit an energy model under Option 1. It appears to me that the reviewers should have advised them at the Design Review stage that Option 3 was not applicable for their project type, not wait until the Construction Review to tell them. With the inexperience of the team, they didn't know that themselves. In the 18-month+ period since registration, that did not come up until the final comment in the Construction review. They have asked for my assistance, and I am really not sure how to approach it. Their questions are: - Should they appeal? - Did the review team mislead them by not alerting them to the primary issue, which is ineligibility for Option 3? (And does that even matter?) - Should they just pay for an energy model and submit under Option 1? Has anyone dealt with a situation like this? Thanks!