Barrett's oesophagus, a pre-malignant condition of the oesophagus has been on a rise in the recent years. The standard diagnostic protocol for Barrett's involves obtaining biopsies at suspicious regions along the oesophagus. The localization and tracking of these biopsy sites " inter-operatively " poses a significant challenge for providing targeted treatments and tracking disease progression. This paper proposes an approach to provide guided navigation and relocalization of the biopsy sites using an electromagnetic tracking system. The characteristic of our approach over existing ones is the integration of an EM sensor at the flexible endoscope tip, so that the endoscopic camera depth inside the oesophagus can be computed in real-time, allowing to retrieve and display an image from a previous exploration at the same depth. We firstly describe our system setup and methodology for inter-operative registration. We then propose three incremental experiments of our approach. First, on synthetic data with realistic noise model to analyze the error bounds of our system. The second on in-vivo pig data using an optical tracking system to provide a pseudo ground-truth. Accuracy results obtained were consistent with the synthetic experiments despite uncertainty introduced due to breathing motion, and remain inside acceptable error margin according to medical experts. Finally, a third experiment designed using data from pigs to simulate a real task of biopsy site relocalization, and evaluated by 10 GI experts. It clearly demonstrated the benefit of our system towards assisted guidance by improving the biopsy site retrieval rate from 47.5% to 94%.