Factual knowledge extraction aims to explicitly extract knowledge parameterized in pre-trained language models for application in downstream tasks. While prior work has been investigating the impact of supervised fine-tuning data on the factuality of large language models (LLMs), its mechanism remains poorly understood. We revisit this impact through systematic experiments, with a particular focus on the factuality gap that arises when fine-tuning on known versus unknown knowledge. Our findings show that this gap can be mitigated at the inference stage, either under out-of-distribution (OOD) settings or by using appropriate in-context learning (ICL) prompts (i.e., few-shot learning and Chain of Thought (CoT)). We prove this phenomenon theoretically from the perspective of knowledge graphs, showing that the test-time prompt may diminish or even overshadow the impact of fine-tuning data and play a dominant role in knowledge extraction. Ultimately, our results shed light on the interaction between finetuning data and test-time prompt, demonstrating that ICL can effectively compensate for shortcomings in fine-tuning data, and highlighting the need to reconsider the use of ICL prompting as a means to evaluate the effectiveness of fine-tuning data selection methods.