I'm making an elevation map and I want to make a path with a gradient fill from one layer to another, and to do so, cut a large section from the center. However, the gradient fill acts as if the path is just being blocked instead of cut. Is there any way to fix this? Thanks in advance! 

Please describe in greater detail... Inkscape layers?... "cutting"?... etc.

Oh sure, by "layers" I was trying to say a series of paths inside each other, then I used difference on each one, so there was a hole in each one. What I'm trying to do is make the gradient change equal around the entire shape, always going form the first stop to the last one to both edges, regardless of distance

Oh sure, by "layers" I was trying to say a series of paths inside each other, then I used difference on each one, so there was a hole in each one. What I'm trying to do is make the gradient change equal around the entire shape, always going form the first stop to the last one to both edges, regardless of distance

If I understand, you would like the fill of a shape like this to be a gradient that follows the centerline between the edges... And the gradient has a different color at the edges (A), or the same color at the edges (B)?

A is what I'm talking about

I'd probably use mesh gradients.

Crude example:

I made this using [Extensions > Generate from Path > Interpolate...] then blurring and clipping the resulting group of paths. My browser (Safari on Mac) doesn't render the contoured gradient effect but it looks good in Inkscape.

Here's an update that renders correctly. I'm not sure what's wrong with my first attempt.