Software applications are becoming highly critical in aircraft development lifecycle. They provide the capability and functionalities required to design, manufacture and support aerospace assets of increasing complexity. As such criticality rises, there is a need to implement monitoring and management techniques on software application portfolios, in order to optimise service performance. These methodologies will support industry activities, avoiding operation disruption and mitigating the systemic risks that come with a higher complexity, as well as controlling obsolescence issues over time. This paper seeks to understand the key challenges faced when monitoring software lifecycle and obsolescence over large software application portfolios in aerospace industry. The paper describes results from a series of interviews and workshops with industry experts, as well as meetings with academic experts and literature reviews, to provide a discerning sight on the challenges faced when managing large application portfolios, in terms of complexity and obsolescence.