Basically, the series of documents are NSA OIG and Congressional reports about the email surveillance program that was shuttered in 2011. It provides a bit more information than was previously available under the original leaks in 2013.
What the author of this article is trying to express is the idea that the NSA was able to resume the function of the email metadata program (they call it PR/TT, or Pen Register / Tap Trace) with some other secret program. The NYT alleges that a paragraph on page 65 links this defunct program with the upstream collection and the PRISM (both FAA §702) programs. It's stated in the paragraph that the NSA concludes that it can do its job with upstream/PRISM and for phone calls, chaining through the telephony metadata collection (SPCMA).
TL;DR: The NSA stopped using the email metadata program and then relied on upstream/PRISM and the telephone metadata program to fulfill the need. The NYT got some FOIA'd documents to confirm this with an official statement.