Accurate seafloor mapping is essential for marine science, archaeology, and environmental monitoring. However, integrating data from different sensors, such as side-scan sonar and optical cameras, collected across separate survey sessions, remains challenging due to positioning drift and sensor offsets. This paper presents a multi-session, multimodal underwater mapping framework based on factor graph optimization. The method jointly optimizes vehicle trajectories, 3D landmark positions, sensor extrinsics, and per-session global alignment transformations. By combining rigid inter-session corrections with local trajectory deformations, it compensates for both inter-session offsets and intra-session distortions from accumulated navigation errors. The proposed methodology was validated on real-world datasets collected along the Catalan coast. Results show measurable improvements in map consistency over both unoptimized and rigid-alignment baselines across all metrics, including Pixel Accuracy and mean Intersection over Union. The method achieves a 3.4% improvement in pixel accuracy over the unoptimized baseline, corresponding to improved semantic labelling across approximately 14700
m2 of mapped area. Qualitative results further show consistent co-registration between sonar and optical maps, even in the presence of significant trajectory distortions and inter-session misalignments. These findings demonstrate the potential of the proposed framework to generate coherent multimodal seafloor maps from heterogeneous underwater surveys.