What's to "prepare" for shutting it down? Reminds me of the story where John Coltrane told Miles Davis that he didn't know how to end his solos. Miles said: "Try taking the fucking horn out of your mouth."
They're not going to shut down a single thing. They need to roll out a half-assed update to 'minimize' data on US persons, and also open investigations of potential criminal activity into as many millions of Americans as possible (because they can keep surveillance on in that case).
They'll probably try to do this as sloppily as possible because as long as they can claim surveillance of US people is unintentional, it's legal under FISA 702.
Nice. I'm sure there must be administrative stuff no? Shuffling employees around. Shutting down servers. Setting up the pipeline to deal with the telcos. Etc. Etc.
But yea, it should be as simple as a switch, the rest is just after effects, you're right.
Depending on which bill passes, if any, they may move to a system where they contact providers and request records on a case-by-case basis... like every law enforcement agency already does. That does require some changes in procedures.
What they have to do is prepare to do their jobs in the absence of the kind of programs that will no longer be authorized. Most likely what that means is they're going to do things like hire a bunch of lawyers to handle an increase in the number of requests they make to FISA courts.
What they're really doing here is what bureaucrats always do when you tell them they can't do something - this is the first step in a PR campaign to scare people into forcing Congress to reauthorize expansive data collection.