Did these updates cause fingerprint change and SSH warning?

I logged in and did a few updates around noon, and when I rebooted and tried to log back in, my WinSCP program screamed “WARNING - POTENTIAL SECURITY BREACH!” I cancelled and tried again every half hour until I finally decided to just override it and login. I looked at the logs and think things seem normal.

The server is a few years old and I have always had password authentication shut off. The keys are 2048 length with password protection them. I am the only person with access to this server. It did NOT have fail2ban installed.

Here is the info on what I updated that may be to blame for the warning.

Start-Date: 2018-09-17  12:22:14
Commandline: apt-get upgrade
Upgrade: linux-virtual-lts-xenial:amd64 (4.4.0.134.140, 4.4.0.135.141), cloud-init:amd64 (18.2-4-g05926e48-0ubuntu1~16.04.2, 18.3-9-g2e62cb8a-0ubuntu1~16.04.2), uuid-runtime:amd64 (2.27.1-6ubuntu3.4, 2.27.1-6ubuntu3.6), libfdisk1:amd64 (2.27.1-6ubuntu3.4, 2.27.1-6ubuntu3.6), linux-libc-dev:amd64 (4.4.0-134.160, 4.4.0-135.161), libmount1:amd64 (2.27.1-6ubuntu3.4, 2.27.1-6ubuntu3.6), snapd:amd64 (2.32.9, 2.34.2), squashfs-tools:amd64 (1:4.3-3ubuntu2.16.04.1, 1:4.3-3ubuntu2.16.04.3), certbot:amd64 (0.25.0-1+ubuntu16.04.1+certbot+1, 0.26.1-1+ubuntu16.04.1+certbot+2), open-iscsi:amd64 (2.0.873+git0.3b4b4500-14ubuntu3.4, 2.0.873+git0.3b4b4500-14ubuntu3.5), python-apt-common:amd64 (1.1.0~beta1ubuntu0.16.04.1, 1.1.0~beta1ubuntu0.16.04.2), udev:amd64 (229-4ubuntu21.2, 229-4ubuntu21.4), initramfs-tools-bin:amd64 (0.122ubuntu8.11, 0.122ubuntu8.12), linux-headers-virtual-lts-xenial:amd64 (4.4.0.134.140, 4.4.0.135.141), libudev1:amd64 (229-4ubuntu21.2, 229-4ubuntu21.4), systemd-sysv:amd64 (229-4ubuntu21.2, 229-4ubuntu21.4), python3-acme:amd64 (0.25.1-1+ubuntu16.04.1+certbot+1, 0.26.0-1+ubuntu16.04.1+certbot+1), ubuntu-core-launcher:amd64 (2.32.9, 2.34.2), shared-mime-info:amd64 (1.5-2ubuntu0.1, 1.5-2ubuntu0.2), libsmartcols1:amd64 (2.27.1-6ubuntu3.4, 2.27.1-6ubuntu3.6), libglib2.0-data:amd64 (2.48.2-0ubuntu1, 2.48.2-0ubuntu4), python3-certbot:amd64 (0.25.0-1+ubuntu16.04.1+certbot+1, 0.26.1-1+ubuntu16.04.1+certbot+2), libjs-sphinxdoc:amd64 (1.3.6-2ubuntu1.1, 1.3.6-2ubuntu1.2), libglib2.0-0:amd64 (2.48.2-0ubuntu1, 2.48.2-0ubuntu4), initramfs-tools-core:amd64 (0.122ubuntu8.11, 0.122ubuntu8.12), initramfs-tools:amd64 (0.122ubuntu8.11, 0.122ubuntu8.12), python3-apt:amd64 (1.1.0~beta1ubuntu0.16.04.1, 1.1.0~beta1ubuntu0.16.04.2), libslang2:amd64 (2.3.0-2ubuntu1, 2.3.0-2ubuntu1.1)
End-Date: 2018-09-17  12:22:46

Start-Date: 2018-09-17  12:23:51
Commandline: apt autoremove
Remove: python3-ndg-httpsclient:amd64 (0.4.2-1+certbot~xenial+1), liblockfile-bin:amd64 (1.09-6ubuntu1), sendmail-cf:amd64 (8.15.2-3), sendmail-base:amd64 (8.15.2-3), liblockfile1:amd64 (1.09-6ubuntu1)
End-Date: 2018-09-17  12:23:52