What would be the best method for saving and loading in my situation

[vast magnet]

So you're saying you have a map creation tool that generates these custom resources for you in runtime, but you're not saving them on disk?

I guess it really depends on what your goal here is. If it's a roguelike/lite where a user will always get a newly generated map upon starting the game but you still want to support them closing the game and reopening it to continue it's one approach. If it's something like a static thing that you want to do once and ship your game with it, it's another approach

If it's the first option, you could look into generating a seed and saving that + data from the already visited rooms. This lets you generate stuff in runtime as the player starts new games but keeps the save relatively light as it's just a seed and some data about what they did. This is how Minecraft does it for example.

If it's the second option, why are you not saving these resources?

[queen garnet]

I was worried about having dozens to thousands of room files clogging up the game, just an unsortable mess.
In my desperation I figured out how to have the game make new folder paths, so now the resources are saved with their id as their name in a folder containing the map name, which I think works well enough, though I'd still love suggestions or advice if there's a better way