Resolution to root cause # 1: The issue is fixed permanently starting from WorldServer 11.3.3.
Workarounds for earlier versions can be found in this article:
WorldServer - Source or target file exist but WorldServer fails to locate it - The asset doesn't exist or has been deleted Resolution to root cause # 2: Rename the source file to a shorter name and add it to the project or create a new project with it. The max path length should not exceed 260 characters with spaces. Add the renamed file to the project or create a new project with it. The
Check In Automatic Action will copy the file to the directory without issues.