When you say “set to not share” what exactly do you mean, how exactly did you set that? You can certainly safely set all users to deny access without issue, but if you removed the share then yes everything will be deleted.
There is also an annoying feature that if you remove a user, any share with the same name is also removed (as such a share is created when the user is created). Normally it’s ok, but if you make a user with the same name as an already existing share then remove, the pre-existing share will get removed too even though it pre-existed.
And I don’t know of any tools you can use to undelete stuff on the MCM, indeed if such exists I’d be interested to know (aside from enabling the recycle bins, but even that I don’t think would have helped in this case).