I'm no lawfag, and I'll be the first to admit that convoluted court filings leave me scratching my head at times, but consider this.
Gleeson's reply brief was originally due to be filed today. Instead he filed the doc to request clarification on whether he should still file, and asked for an extension, if so. With Sullivan's stay order, Gleeson will not be filing the reply brief, without Sullivan actually having to respond to Gleeson. Not sure what else would be the effect, but that popped into my head.