There are Regulations and Policies in place in all federal agencies to mandate the saving of electronic communications called the Federal Records Act. ALL email communications do not just happen on a local hard drive, theses messages are relayed through multiple systems, which are backed up and archived as a matter of practice and of federal law. 
Under Records management regulations (44 U.S.C ch. 31 ss3101 *) there are specific procedures and duties that agency heads are required to know.
Lois Lerner would have been REQUIRED BY LAW to know these policies, exercise and enforce them.
It is ILLEGAL for Federal employees to delete any electronic communication without written permission from supervisors, and simply doing so on a local hard drive would not have deleted the message from the archived server, unless others knowingly conspired to remove them.
Other agencies have been caught using eternal, "secret" email addresses, including the former head of HHS, Kathleen Sebelius. It is a clear pattern of this administration to obfuscate, misdirect, lie, deceive and hide it's activities across multiple agencies.
While the Obama administration continues their corrupt behavior our Republican "leaders" in Washington have done as little to use their Constitutional power to protect the American Public. This direct attack on our First Amendment right of free political speech is the most egregious attack on the First Amendment since the Alien and Sedition Acts.

The issue here is not missing data but missing itegrity on the part of the administration, this is certinly something that cannot be recovered without a change in personelle.