Se você não se importa em usar o perl:
perl -pe 's/^(.*?):(\d+): error: undefined reference to (.*)/\t\t/g'
A saída do seu exemplo ficaria assim:
out/target/product/gen/SHARED_LIBRARIES/libfishy_proto_intermediates/proto/base/fishy/fishy/prefix/fishy_proto/service_registry.pb.h 408 'fishy_proto::Service::CopyFrom(fishy_proto::Service const&)'
base/fishy/fishy/impl/service.cpp 448 'fishy_proto::Service::Service()'
base/fishy/fishy/impl/service.cpp 489 'fishy_proto::Service::~Service()'
base/fishy/fishy/impl/service.cpp 489 'fishy_proto::Service::~Service()'
base/fishy/fishy/impl/service_registry.cpp 51 'fishy_proto::ServiceList::ServiceList()'
base/fishy/fishy/impl/service_registry.cpp 51 'fishy_proto::ServiceList::~ServiceList()'
base/fishy/fishy/impl/service_registry.cpp 51 'fishy_proto::ServiceList::~ServiceList()'
base/fishy/fishy/impl/service_registry.cpp 51 'fishy_proto::ServiceList::~ServiceList()'
base/fishy/fishy/impl/service_registry.cpp 51 'fishy_proto::ServiceList::~ServiceList()'
base/fishy/fishy/impl/service_registry.cpp 279 'fishy_proto::Request::Request()'
base/fishy/fishy/impl/service_registry.cpp 319 'fishy_proto::Request::~Request()'
base/fishy/fishy/impl/service_registry.cpp 319 'fishy_proto::Request::~Request()'
base/fishy/fishy/impl/service_registry.cpp 722 'fishy_proto::Request::Request()'
out/target/product/phaedra/gen/SHARED_LIBRARIES/libfishy_proto_intermediates/proto/base/fishy/fishy/prefix/fishy_proto/service_registry.pb.h 72 'fishy_proto::Request_Type_descriptor()'
base/fishy/fishy/impl/service_registry.cpp 762 'fishy_proto::Request::~Request()'
base/fishy/fishy/impl/service_registry.cpp 762 'fishy_proto::Request::~Request()'
base/fishy/fishy/impl/service_registry.cpp 463 'fishy_proto::Service::Service()'
base/fishy/fishy/impl/service_registry.cpp 500 'fishy_proto::Service::~Service()'
base/fishy/fishy/impl/service_registry.cpp 500 'fishy_proto::Service::~Service()'
external/protobuf/src/google/protobuf/arena.h 649 'fishy_proto::ServiceGroup::ServiceGroup()'
external/protobuf/src/google/protobuf/arena.h 309 'fishy_proto::ServiceGroup::ServiceGroup()'
external/protobuf/src/google/protobuf/arena.h 649 'fishy_proto::Service::Service()'
external/protobuf/src/google/protobuf/arena.h 309 'fishy_proto::Service::Service()'