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Allow Metadata Save Operations to Complete with Returned Warnings
When a metadata save operation generates warnings, the default behavior of Tooling API
is to fail the operation without returning the warnings. For objects in both the Tooling API and
Metadata API WSDLs, you can indicate that you want error-free save operations to complete
successfully, returning any warnings.
To indicate that you want error-free save operations to complete successfully, returning any generated warnings, specify the header ignoreSaveWarnings in your HTTP request.
There is also a SOAP header in Tooling API for saving metadata even if warnings are returned. See MetadataWarningsHeader.