I only have a testcase for Bionic, I hope rbalint has one for the other releases.


root@b:~# apt list --upgradable
Listing... Done
qemu-guest-agent/bionic-updates,bionic-security 1:2.11+dfsg-1ubuntu7.12 amd64 [upgradable from: 1:2.11+dfsg-1ubuntu7]
N: There is 1 additional version. Please use the '-a' switch to see it
root@b:~# 
root@b:~# 
root@b:~# sudo unattended-upgrade -d
Initial blacklisted packages: 
Initial whitelisted packages: 
Starting unattended upgrades script
Allowed origins are: o=Ubuntu,a=bionic, o=Ubuntu,a=bionic-security, o=UbuntuESM,a=bionic
Using (^linux-image-[0-9]+\.[0-9\.]+-.*|^linux-headers-[0-9]+\.[0-9\.]+-.*|^linux-image-extra-[0-9]+\.[0-9\.]+-.*|^linux-modules-[0-9]+\.[0-9\.]+-.*|^linux-modules-extra-[0-9]+\.[0-9\.]+-.*|^linux-signed-image-[0-9]+\.[0-9\.]+-.*|^kfreebsd-image-[0-9]+\.[0-9\.]+-.*|^kfreebsd-headers-[0-9]+\.[0-9\.]+-.*|^gnumach-image-[0-9]+\.[0-9\.]+-.*|^.*-modules-[0-9]+\.[0-9\.]+-.*|^.*-kernel-[0-9]+\.[0-9\.]+-.*|^linux-backports-modules-.*-[0-9]+\.[0-9\.]+-.*|^linux-modules-.*-[0-9]+\.[0-9\.]+-.*|^linux-tools-[0-9]+\.[0-9\.]+-.*|^linux-cloud-tools-[0-9]+\.[0-9\.]+-.*) regexp to find kernel packages
Using (^linux-image-4\.15\.0\-48\-generic$|^linux-headers-4\.15\.0\-48\-generic$|^linux-image-extra-4\.15\.0\-48\-generic$|^linux-modules-4\.15\.0\-48\-generic$|^linux-modules-extra-4\.15\.0\-48\-generic$|^linux-signed-image-4\.15\.0\-48\-generic$|^kfreebsd-image-4\.15\.0\-48\-generic$|^kfreebsd-headers-4\.15\.0\-48\-generic$|^gnumach-image-4\.15\.0\-48\-generic$|^.*-modules-4\.15\.0\-48\-generic$|^.*-kernel-4\.15\.0\-48\-generic$|^linux-backports-modules-.*-4\.15\.0\-48\-generic$|^linux-modules-.*-4\.15\.0\-48\-generic$|^linux-tools-4\.15\.0\-48\-generic$|^linux-cloud-tools-4\.15\.0\-48\-generic$) regexp to find running kernel packages
Checking: qemu-guest-agent ([<Origin component:'universe' archive:'bionic-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>, <Origin component:'universe' archive:'bionic-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>])
pkgs that look like they should be upgraded: qemu-guest-agent
Get:1 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 qemu-guest-agent amd64 1:2.11+dfsg-1ubuntu7.12 [232 kB]                                                                 
Fetched 232 kB in 0s (0 B/s)                                                                                                                                                                 
fetch.run() result: 0
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 0 IsTrusted: 1 FileSize: 232116 DestFile:'/var/cache/apt/archives/qemu-guest-agent_1%3a2.11+dfsg-1ubuntu7.12_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/universe/q/qemu/qemu-guest-agent_2.11+dfsg-1ubuntu7.12_amd64.deb' ID:1 ErrorText: ''>
check_conffile_prompt(/var/cache/apt/archives/qemu-guest-agent_1%3a2.11+dfsg-1ubuntu7.12_amd64.deb)
found pkg: qemu-guest-agent
conffile line: /etc/init.d/qemu-guest-agent f61a64ac1e48993023018fd1cff85191
current md5: f61a64ac1e48993023018fd1cff85191
conffile line: /etc/qemu/fsfreeze-hook/fsfreeze-hook 15f6ff42cbc5550a07ee21c2a471d905
/etc/qemu/fsfreeze-hook/fsfreeze-hook not in package conffiles /etc/init.d/qemu-guest-agent
/etc/qemu/fsfreeze-hook
found conffile /etc/qemu/fsfreeze-hook in new pkg but on dpkg status
Traceback (most recent call last):
  File "/usr/bin/unattended-upgrade", line 2057, in <module>
    sys.exit(main(options))
  File "/usr/bin/unattended-upgrade", line 1773, in main
    if conffile_prompt(item.destfile):
  File "/usr/bin/unattended-upgrade", line 988, in conffile_prompt
    with open(prefix + conf_file, 'rb') as fp:
IsADirectoryError: [Errno 21] Is a directory: '/etc/qemu/fsfreeze-hook'

That is good, it means that the error is affecting this system.
After installing the new unattended upgrades from proposed this works fine now:

root@b:~# apt list --upgradable
Listing... Done
qemu-guest-agent/bionic-updates,bionic-security 1:2.11+dfsg-1ubuntu7.12 amd64 [upgradable from: 1:2.11+dfsg-1ubuntu7]
N: There is 1 additional version. Please use the '-a' switch to see it
root@b:~# sudo unattended-upgrade -d
Initial blacklisted packages: 
Initial whitelisted packages: 
Starting unattended upgrades script
Allowed origins are: o=Ubuntu,a=bionic, o=Ubuntu,a=bionic-security, o=UbuntuESM,a=bionic
Using (^linux-image-[0-9]+\.[0-9\.]+-.*|^linux-headers-[0-9]+\.[0-9\.]+-.*|^linux-image-extra-[0-9]+\.[0-9\.]+-.*|^linux-modules-[0-9]+\.[0-9\.]+-.*|^linux-modules-extra-[0-9]+\.[0-9\.]+-.*|^linux-signed-image-[0-9]+\.[0-9\.]+-.*|^kfreebsd-image-[0-9]+\.[0-9\.]+-.*|^kfreebsd-headers-[0-9]+\.[0-9\.]+-.*|^gnumach-image-[0-9]+\.[0-9\.]+-.*|^.*-modules-[0-9]+\.[0-9\.]+-.*|^.*-kernel-[0-9]+\.[0-9\.]+-.*|^linux-backports-modules-.*-[0-9]+\.[0-9\.]+-.*|^linux-modules-.*-[0-9]+\.[0-9\.]+-.*|^linux-tools-[0-9]+\.[0-9\.]+-.*|^linux-cloud-tools-[0-9]+\.[0-9\.]+-.*) regexp to find kernel packages
Using (^linux-image-4\.15\.0\-48\-generic$|^linux-headers-4\.15\.0\-48\-generic$|^linux-image-extra-4\.15\.0\-48\-generic$|^linux-modules-4\.15\.0\-48\-generic$|^linux-modules-extra-4\.15\.0\-48\-generic$|^linux-signed-image-4\.15\.0\-48\-generic$|^kfreebsd-image-4\.15\.0\-48\-generic$|^kfreebsd-headers-4\.15\.0\-48\-generic$|^gnumach-image-4\.15\.0\-48\-generic$|^.*-modules-4\.15\.0\-48\-generic$|^.*-kernel-4\.15\.0\-48\-generic$|^linux-backports-modules-.*-4\.15\.0\-48\-generic$|^linux-modules-.*-4\.15\.0\-48\-generic$|^linux-tools-4\.15\.0\-48\-generic$|^linux-cloud-tools-4\.15\.0\-48\-generic$) regexp to find running kernel packages
Checking: qemu-guest-agent ([<Origin component:'universe' archive:'bionic-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>, <Origin component:'universe' archive:'bionic-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>])
pkgs that look like they should be upgraded: qemu-guest-agent
Fetched 0 B in 0s (0 B/s)                                                                                                                                                                    
fetch.run() result: 0
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 232116 DestFile:'/var/cache/apt/archives/qemu-guest-agent_1%3a2.11+dfsg-1ubuntu7.12_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/universe/q/qemu/qemu-guest-agent_2.11+dfsg-1ubuntu7.12_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt(/var/cache/apt/archives/qemu-guest-agent_1%3a2.11+dfsg-1ubuntu7.12_amd64.deb)
found pkg: qemu-guest-agent
conffile line: /etc/init.d/qemu-guest-agent f61a64ac1e48993023018fd1cff85191
current md5: f61a64ac1e48993023018fd1cff85191
conffile line: /etc/qemu/fsfreeze-hook/fsfreeze-hook 15f6ff42cbc5550a07ee21c2a471d905
current md5: 15f6ff42cbc5550a07ee21c2a471d905
blacklist: []
whitelist: []
Packages that will be upgraded: qemu-guest-agent
Writing dpkg log to /var/log/unattended-upgrades/unattended-upgrades-dpkg.log
applying set ['qemu-guest-agent']
(Reading database ... 47684 files and directories currently installed.)
Preparing to unpack .../qemu-guest-agent_1%3a2.11+dfsg-1ubuntu7.12_amd64.deb ...
Unpacking qemu-guest-agent (1:2.11+dfsg-1ubuntu7.12) over (1:2.11+dfsg-1ubuntu7) ...
Processing triggers for ureadahead (0.100.0-21) ...
Setting up qemu-guest-agent (1:2.11+dfsg-1ubuntu7.12) ...
Processing triggers for systemd (237-3ubuntu10.21) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
left to upgrade set()
All upgrades installed
InstCount=0 DelCount=0 BrokenCount=0
Extracting content from /var/log/unattended-upgrades/unattended-upgrades-dpkg.log since 2019-04-30 11:16:20
root@b:~# apt list --upgradable
Listing... Done


Setting Bionic to verified.