When a Clean is performed on a code project that uses a binary Engine installation on a Mac, some of the Engine's .dylib files are removed during the Clean process. A Clean process for a project using a binary Engine installation should not affect any of the Engine files. This does not occur for projects on Windows.
The build fails due to several missing Engine .dylib files.
The build completes successfully.
Verify the binary Engine files, which will replace the missing .dylib files, then build the project in Xcode.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-59295 in the post.