Pulling from Flywheel deletes WP core files and breaks local install

What issue or error are you experiencing?

Recently when I pull an existing site from Flywheel down to local it can sometimes break the local install completely. I get an error message (screenshot below), and then when I check the file structure only wp-content is left — all other WP folders are deleted (another screenshot below).

Trying again on a new install does not solve the problem and I am currently unable to access these sites at all locally. This is destroying my workflow and I’m at my wits end.



System Details

  • Local Version: Version 9.2.9+6887

  • Operating System (OS) and OS version: macOS Sequoia 15.5