The agency issued a statement Thursday notifying the public that in May it began to delete all so-called "call detail records" (CDRs) collected since 2015.
CDRs are handed over by telecommunications providers, and contain metadata - including phone numbers as well as the time and duration of phone calls. The actual content of the calls themselves is not monitored by this system. Skype (and therefore Microsoft), however, provides a bit more to the US Government as revealed by Edward Snowden - handing the NSA "buddy lists, credit card data, call records and user account information," and possibly the plaintext inside of messages, according to Arstechnica.
"NSA is deleting the CDRs because several months ago NSA analysts noted technical irregularities in some data received from telecommunications service providers," said the NSA.