Should I make separate current affairs notes for Prelims and Mains for UPSC?

You should not make entirely separate notes for Prelims and Mains. Instead, adopt an integrated strategy where you store facts and analysis in a single location. Since the topics are largely the same, separating them leads to redundant work and a fragmented understanding.
The key is to change how you record information. For Prelims, you need objective data—such as the name of a ministry, specific penalties in a Bill, or the location of a summit. For Mains, you need the why and how—the pros and cons, the socio-economic impact, and a way forward.
A split-note format (ideal for digital tools like OneNote) is the most efficient. Under one header, such as the "Data Protection Bill," create a Facts Box for Prelims-specific data and an Analysis Section for Mains arguments. Always include a Static Link, like the relevant Constitutional Article or a landmark Supreme Court case.
This approach saves time by avoiding double entries and ensures that when you transition to Mains preparation after the Prelims, your analytical fodder is already organized and ready. Integrating the two stages allows the deeper context of the Mains to help you naturally remember the dry facts required for the Prelims.