We know that Coulson won't tell her the truth, but I can't remember what the document actually ends up saying? Did it provide different info than the ex-SHIELD agent Coulson and May picked up for interviewing?
The redacted document seen on-screen was an internal SHIELD memo detailing the results of a medical exam performed on baby Skye at the orphanage.
The letterhead on the page leads us to believe it was written from within St. Agnes Orphanage, indicating that at least one SHIELD agent was undercover at the orphanage to keep tabs on Skye.
There were apparently other pages contained in the file (at least one of which apparently identified the gender of the agent who delivered Skye to the orphanage), but the medical results memo is the only document shown on-screen: