I think this now may be possible with the list_merge_mode param in OmegaConf.merge(): https://github.com/omry/omegaconf/blob/117f7de07285e4d1324b9229eaf873de15279457/omegaconf/omegaconf.py#L261. You can create one config from your YAML file, and another from OmegaConf.from_cli(arg_list), and merge the two with the EXTEND option. Note that this currently isn't possible with OmegaConf.update(), as the list_merge_mode param isn't exposed there. I mention that here: https://github.com/omry/omegaconf/issues/1154#issuecomment-2655401555