Well, maybe a start at an answer for you. Yes, because of the construction. But I've been thru LIM a few times recently and they seem to be dealing with it pretty well, I think they clear the flights before shutting it down for the night.
Not sure I'd be too worried right now, the connect is pretty fast thru the sterile area, sometimes a bit of a line but they'd put you to the front if you asked, and you can print your boarding pass 48 hours before (when you are in Ecuador) for protection as well... maybe others have opinions