Apps are removed from the dock when the app is replaced as part of an upgrade

[SteppingHat]

• I understand that if I ignore these instructions, my issue may be closed without review.
• I have retried my command with --force.
• I ran brew update-reset && brew update and retried my command.
• I ran brew doctor, fixed as many issues as possible and retried my command.
• I have checked the instructions for reporting bugs.
• I made doubly sure this is not a checksum does not match error.

Description of issue

When using brew to upgrade casks, apps are removed from the dock (if they are present) when brew reaches the Removing App step of the upgrade process.
Once the app is removed from the /Applications directory, it is immediately removed from the dock, before brew has moved the downloaded cask to the applications directory.

If I recall correctly, icons would turn into a ? once clicked if the path was no longer valid. I am experiencing this on macOS 11.3, however I'm not able to confirm if there was a change in macOS 11.x or a prior release that causes the dock to now remove items from the dock once they are missing on the system.

Regardless, this should now be something that brew should take into account when upgrading casks.

The upgrade itself runs just fine and the app is upgraded successfully, however it must be manually re-added to the dock.
This has been tested on multiple machines and is always reproducible.

Command that failed

brew upgrade --cask --greedy

Output of command with --verbose --debug

Click to expand

==> Upgrading 6 outdated packages:

coconutbattery 3.9.5,f4c29259 -> 3.9.5,4891c16e

google-chrome 90.0.4430.212 -> 91.0.4472.77

iterm2 3.4.6 -> 3.4.8

obs 26.1.2 -> 27.0

==> Upgrading coconutbattery

==> Downloading https://www.coconut-flavour.com/downloads/coconutBattery_395_4891c16e.zip

######################################################################## 100.0%

==> Removing launchctl service com.coconut-flavour.coconutBattery-Menu

==> Backing App 'coconutBattery.app' up to '/usr/local/Caskroom/coconutbattery/3.9.5,f4c29259/coconutBat

==> Removing App '/Applications/coconutBattery.app'

==> Moving App 'coconutBattery.app' to '/Applications/coconutBattery.app'

==> Purging files for version 3.9.5,f4c29259 of Cask coconutbattery

🍺  coconutbattery was successfully upgraded!

...etc

Output of brew doctor --verbose

Click to expand

==> Cask Environment Variables:

BUNDLE_PATH

CHRUBY_VERSION

GEM_HOME

GEM_PATH

HOMEBREW_CASK_OPTS

LC_ALL

PATH

RBENV_VERSION

RUBYLIB

RUBYOPT

RUBYPATH

SHELL

==> $LOAD_PATHS

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/warning-1.2.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/tapioca-0.4.23/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/spoom-1.0.9/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/thor-1.1.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/sorbet-runtime-stub-0.2.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/simplecov-cobertura-1.4.2/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/simplecov-0.21.2/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/simplecov_json_formatter-0.1.2/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/simplecov-html-0.12.3/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/ruby-macho-2.5.1/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rubocop-sorbet-0.6.2/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rubocop-rspec-2.3.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rubocop-rails-2.10.1/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rubocop-performance-1.11.3/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rubocop-1.16.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/unicode-display_width-2.0.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/ruby-progressbar-1.11.0/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-wait-0.0.9/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-sorbet-1.8.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/sorbet-0.5.6274/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/sorbet-static-0.5.6274-universal-darwin-14/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-retry-0.6.2/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-3.10.0/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-mocks-3.10.2/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-expectations-3.10.1/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/rspec-support-3.10.2/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/mini_portile2-2.5.3/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/hpricot-0.8.6/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/elftools-1.1.3/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/domain_name-0.5.20190701/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/unf_ext-0.0.7.7/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/extensions/x86_64-darwin-14/2.6.0-static/unf_ext-0.0.7.7

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/docile-1.3.5/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/bootsnap-1.7.5/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/msgpack-1.4.2/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/ast-2.4.2/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/public_suffix-4.0.6/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/activesupport-6.1.3.2/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/zeitwerk-2.4.2/lib

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/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/i18n-1.8.10/lib

/usr/local/Homebrew/Library/Homebrew/vendor/bundle/bundler/../ruby/2.6.0/gems/concurrent-ruby-1.1.9/lib/concurrent-ruby

/Library/Ruby/Site/2.6.0

/Library/Ruby/Site/2.6.0/x86_64-darwin20

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/Library/Ruby/Site

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/vendor_ruby/2.6.0

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/vendor_ruby/2.6.0/x86_64-darwin20

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/vendor_ruby/2.6.0/universal-darwin20

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/vendor_ruby

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/x86_64-darwin20

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/universal-darwin20

/usr/local/Homebrew/Library/Homebrew

==> Homebrew Version

3.1.11

==> macOS

11.3.1

==> SIP

Enabled

==> Homebrew Cask Staging Location

/usr/local/Caskroom

==> Homebrew Cask Taps:

/usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask (3919 casks)

Please note that these warnings are just used to help the Homebrew maintainers

with debugging if you file an issue. If everything you use Homebrew for is

working fine: please don't worry or file an issue; just ignore this. Thanks!
Warning: Some installed formulae are deprecated or disabled.

You should find replacements for the following formulae:

ilmbase

Output of brew tap

Click to expand

dart-lang/dart

homebrew/cask

homebrew/core

sass/sass

[cho-m]

I think this is a duplicate of #102721, which has a discussion on potential solution.