The servers being taken out of commission, etc. resulted in loss of emails on those servers. As he described in one case the email system was deleted, so the data was fragmented. This happened over time. However, it is thought Clinton likely preserved some of the emails and transitioned them to the next server.
Hence his statement later about the purging by the lawyers, which he places in 2014, but for which there is no definitive date.
The lawyers doing the sorting for Secretary Clinton in 2014 did not individually read the content of all of her e-mails, as we did for those available to us; instead, they relied on header information and used search terms to try to find all work-related e-mails among the reportedly more than 60,000 total e-mails remaining on Secretary Clinton’s personal system in 2014. It is highly likely their search terms missed some work-related e-mails, and that we later found them, for example, in the mailboxes of other officials or in the slack space of a server.
Hillary's head lawyer and another lawyer on staff received security clearance in late 2014, November and December respectively.
Either way, it ls likely this purge happened in late 2014.
Per this CNN article Gowdy requested the emails in December 2014, around that time frame.
http://www.cnn.com/2015/07/08/politics/hillary-clinton-benghazi-subpoena-gowdy/
Incidentally she was supposed to turn over records in her possession when she left the State Department. Certainly the deletions were after that.
And as I said, either way, she was supposed to preserve all documents, not delete work related documents. It is clear from the IG report and Comey's report she did not turn over all records, which she was required to do. She simply benefited politically from the fact that FOIA compliance was not investigated as part of Comey's team's work because it was out of the scope of the initial request.