The bureau told Congress on Friday that it had uncovered new emails related to the Clinton case — one federal official said they numbered in the THOUSANDS .... (emphasis mine)
http://www.nytimes.com/2016/10/29/us/politics/fbi-hillary-clinton-email.html
If I had to guess, they are Hillary’s e-mails to Huma. Most likely Weiner’s phone was backed up to the cloud or with the same password as Huma’s.