I think there are two separate things I want to address here:

First, agile isn't a project management methodology, it's just a set of 4 abstract priorities and 12 abstract principles. It's very short, you can check it out here:

https://agilemanifesto.org/

Nothing here says that you're not allowed to write documentation, write down requirements, etc. In fact, the principles encourage you yourself as a software team to create the exact processes and documentation that you need in order to meet your goals.

"Working software over comprehensive documentation" does not mean you aren't allowed to have documentation, it just means that you should only write documentation if it helps you build working software, rather than writing documentation for the sake of bureaucracy.

"Individuals and interactions over processes and tools" does not mean that you should have no processes, it just means that the individuals in your team should be empowered to collaboratively create whatever processes you need to deliver good software.

Secondly, in terms of practical advice:

1. Talk about this problem with your team. Is it hard for others to figure out where requirements came from? Maybe they already have a good method and can share it with you. If it's hard for everybody, then propose improvements to your process, for example, propose some type of design document process as part of building any new features
2. There are no perfect answers to the question of "how do I safely make non-trivial changes to systems", but the general approach is to ensure that:

a. You have metrics about how your system is used.

b. You have automated tests covering any requirements, so that you can feel confident when making changes to one part of the system that it isn't violating any unrelated requirements.

c. You actually document any confusing parts in the code itself using comments. The most important thing to cover in comments is "why is this logic necessary?" - whenever something is confusing, you need to answer this question with a comment. Otherwise, the system becomes very annoying to change later on.

If you are missing any of the above, then propose to your team that you start doing it ASAP

3. At the end of the day, somebody is responsible for making product decisions. Is it your team? Or maybe some separate product owner? Sometimes, you just need to communicate with whoever is responsible to figure out if any requirements are still relevant, or if they are now safe to change.