Ok I found the package needed, this command fixes the issue:
sudo apt-get install libgtk2.0-0:i386

It pulls a lot of 32-bit libraries and then Skype can get the proper
themes and colors, included high contrast ones. I am not sure if there
is a smaller subset of libraries needed, but this is what I found to fix
the issue.

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https://bugs.launchpad.net/bugs/1263127

Title:
  hi-contract icons not visible

Status in “gnome-icon-theme-symbolic” package in Ubuntu:
  New
Status in “skype” package in Ubuntu:
  New

Bug description:
  Unable to see the skype icon through the hi-contrast theme

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https://bugs.launchpad.net/ubuntu/+source/gnome-icon-theme-symbolic/+bug/1263127/+subscriptions

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