Why the MTA can't do this kills me and partially explains why people screamed bloody murder about a complete shutdown. The signaling system alone is held together by the equivalent of tape and chewing gum.
https://ny.curbed.com/2018/3/29/17176200/new-york-subway-sig...
If I was in his shoes I would have just said, "Either deal with the loss of the L line, or agree to tolerate a less than 24/7/365 operating schedule." Alas, the L is the only line I know of which uses PTC, which is designed to alleviate some of these issues.
There is no third option.