Compact Layouts Are Changed After Rethink Update
Every time a Rethink update is pushed out, any customizations to Compact Layouts will be overwritten. As a result, the system admin must manually add the desired fields back onto the Compact Layouts.
It turns out this is the behavior that Salesforce has chosen for package upgrades.
Page Layouts themselves are NOT upgradeable (they would not change), but Compact Layouts are upgradeable and so they will be overwritten as new versions are pushed out.
See this Salesforce idea for details: https://ideas.salesforce.com/s/idea/a0B8W00000GdVgXUAV/in-a-package-protect-compact-layout-from-subscriber-changes
There's nothing that can be done to prevent this from happening in the future because Compact Layouts must be in the package when an upgrade is pushed out.
To circumvent this, Buildout can add your company to the 'do not upgrade' list, but this isn't recommended unless absolutely necessary - as you'll want to take advantage of future bug fixes and updates.