That part of the article isn't especially clear:
"Herrera began light training last week and the club believes it can find a way to put him back on the roster in time for the MLS Cup Playoffs. The most straightforward way to do that would have been to acquire an international spot. Instead, a league spokesperson confirmed that the replacement player would need to be removed from the roster in order for the original player to be eligible."
Was the league spokesperson refereing to a Season-Ending Injury Replacement Player? Herrera wasn't eligible for that because his injury occurred outside the Primary Transfer Window. And if NYCFC put him on the Season-Ending Injury List—as they would have had to do to free up his roster slot—he's ineligible to come back this year, plain and simple.* So it's hard to make sense of any of this.
*Okay fine it's not totally simple: NYCFC could argue that the rule prohibiting him from returning to "any remaining competition during that MLS season" doesn't include the postseason. But that doesn't sound like a winner.