If your bag gets very wet in heavy rain, it is rare for a stain to remain on the wet area once it dries.

(In most cases, nothing remains if the rain is light.)

To prevent stains, you can deliberately moisten the entire surface. Moisten the whole item with a wet cloth, as if coloring in the darkened areas. (Wipe lightly, as rubbing too hard will cause the color to fade.)

You might be hesitant to moisten leather, but it's fine as leather is soaked in water during the manufacturing process anyway.

Once it is completely damp, allow it to air dry naturally. This will almost entirely prevent any lingering stains. As the moisture evaporates, the natural oils in the leather will also dissipate, so it is important to apply oil after it has dried.