Many sequences in P5R are not deleted exactly—they're inaccessible. They're in game, theoretically, but game mechanics make it impossible for you ever to see them.
For instance, there are a bunch of TV shows that exist, that are presumably in game, but you can't ever get to the TV to watch them—usually because Morgana makes it impossible for you to go downstairs.
A couple of these scenes happen around the end of Shido's Palace, around the Akechi fight. Once you go into the engine room, you cannot leave until you defeat Akechi. You can't use a Goho-M, you can't take the route out. You are well and truly stuck.
Plus, once you have defeated him, the game funnels you to the Treasure, and any attempt to (say) go to a safe room will again be cockblocked by Morgana.
This means that the last two safe room meetings in Shido's Palace are never accessible. And one of them is important. Let's have a look.
We all know about the meetings—you go to the table in the safe room, you talk to the team, you ask how your progress is. They say some shit. It's usually worth a regular check-in:
The first inaccessible script appears to be triggered by entering the engine room. You get it after going in, but before fighting the Cleaner—so presumably after fighting his mooks, while you chase him about:
Morgana: We found the engine room, so all we need to do now is get our hands on the letter of introduction.
Haru: It would be nice if we could avoid a fight in the process...
Yusuke: Hm, given his attitude up to this point, that is highly unlikely...
The second one appears to kick in after the Akechi fight. After Akechi has given his life to save you:
Yusuke: Goro Akechi... I believe he may have been the greatest casualty of Shido's actions...
Makoto: Was there no other way?
Ann: We'll avenge him when we take Shido down. Come on, we have the letters now—let's do this!
"the greatest casualty of Shido's actions", huh? And it's inaccessible, of course. Leaving the engine room will warp you to the locked treasure room door. If you run to a safe room, Morgana won't let you go in. If you try afterwards, you've been updated to the "we need to send the calling card" script. You never see this.
But I'd bet money it's there. Just out of reach. Just another instance of the PTs understanding Akechi, and mourning him, rather than (say) hating him and being glad he's gone.
one more thing
Most people probably know that you can lurk mournfully by the shutters in the engine room. Nonetheless, here it is: