I'm getting a strange pop in issue after increasing the size of the terrain. This was not an issue before the size increase, so I'm thinking it's got something to do with either the depth buffer or the far planes.
I'm including a video of what it looks like and some code snippets from what I think are relevant places.

Depth buffer

	//create depth stencil texture
	D3D11_TEXTURE2D_DESC descDepth;

	descDepth.Width = mClientWidth;
	descDepth.Height = mClientHeight;
	descDepth.MipLevels = 1;
	descDepth.ArraySize = 1;
	descDepth.Format = DXGI_FORMAT_D32_FLOAT;
	descDepth.SampleDesc.Count = 1;
	descDepth.SampleDesc.Quality = 0;
	descDepth.Usage = D3D11_USAGE_DEFAULT;
	descDepth.BindFlags = D3D11_BIND_DEPTH_STENCIL;
	descDepth.CPUAccessFlags = 0;
	descDepth.MiscFlags = 0;

	if (FAILED(mD3DDevice->CreateTexture2D(&descDepth, NULL, &mD3D11DepthStencilTexture))) return;
	if (FAILED(mD3DDevice->CreateDepthStencilView(mD3D11DepthStencilTexture, 0, &mD3D11DepthStencilView))) return;

Viewport

//set view port ===================================================
	mD3D11Viewport.Width = swapChainDesc.BufferDesc.Width;
	mD3D11Viewport.Height = swapChainDesc.BufferDesc.Height;
	mD3D11Viewport.MinDepth = 0.0f;
	mD3D11Viewport.MaxDepth = 1.0f;
	mD3D11Viewport.TopLeftX = 0;
	mD3D11Viewport.TopLeftY = 0;

	mDeviceContext->RSSetViewports(1, &mD3D11Viewport);

Blend state

D3D11_BLEND_DESC BlendDesc;
	ZeroMemory(&BlendDesc, sizeof(D3D11_BLEND_DESC));

	

	BlendDesc.RenderTarget[0].BlendEnable = TRUE;
	BlendDesc.RenderTarget[0].SrcBlend = D3D11_BLEND_SRC_ALPHA;
	BlendDesc.RenderTarget[0].DestBlend = D3D11_BLEND_INV_SRC_ALPHA;
	BlendDesc.RenderTarget[0].BlendOp = D3D11_BLEND_OP_ADD;
	BlendDesc.RenderTarget[0].SrcBlendAlpha = D3D11_BLEND_ZERO;
	BlendDesc.RenderTarget[0].DestBlendAlpha = D3D11_BLEND_ZERO;
	BlendDesc.RenderTarget[0].BlendOpAlpha = D3D11_BLEND_OP_ADD;
	BlendDesc.RenderTarget[0].RenderTargetWriteMask = D3D11_COLOR_WRITE_ENABLE_ALL;

	mD3DDevice->CreateBlendState(&BlendDesc, &mD3D11BlendState);
	mDeviceContext->OMSetBlendState(mD3D11BlendState, 0, 0xffffffff);

Clearing the depth buffer

// Clear the back buffer 
	float clearColor[4] = { 0.0f, 0.125f, 0.3f, 1.0f }; // red,green,blue,alpha
	mDeviceContext->ClearRenderTargetView(mD3D11RenderTargetView, clearColor);
	mDeviceContext->ClearDepthStencilView(mD3D11DepthStencilView, D3D11_CLEAR_DEPTH, 1, 1);

Projection matrix calculation

	mProjectionMatrix = XMMatrixPerspectiveFovLH(3.14159265f / 4.0f, 4.0f/3.0f, 0.01f, 100000.0f);

Any ideas what this could be?

After doing some additional tests, I think the issue can be narrowed down even further. If I don't draw the skybox, the environement comes out looking better, I can see further, but there are still transparancy issues. I've tried disabling blending but it did not help.

Also when I view the outputs of pixel shaders and output merger states they both display the geometry properly, but I guess something after the output merger stage prevents it from being displayed?

You can see it throughout the video as little pop-ins but the effect becomes jarring at 0:40, at the end I show what the outputs of various stages look like.

Off the top of my head its either z-buffer, alpha blending or back face culling. It looks more like z-buffer.

In ClearDepthStencilView why do you set stencil to 1? Don't think it matters though.

Try narrowing the near far clip range to make sure its not a z-buffer fighting thing. 0.001 to 100000 is a pretty big range.

29 minutes ago, TeaTreeTim said:

Off the top of my head its either z-buffer, alpha blending or back face culling. It looks more like z-buffer.

In ClearDepthStencilView why do you set stencil to 1? Don't think it matters though.

 Try narrowing the near far clip range to make sure its not a z-buffer fighting thing. 0.001 to 100000 is a pretty big range.

  

That was it! Thanks so much, I raised the low clip to 10 and it fixed the clipping issue. I had to increase the skybox radius as well and now it looks great. 

For a skybox, a trick you can use is to force its depth to the far clip plane. This will keep it from drawing on top of your scene geometry without having to use crazy long draw distances. The easiest way to do it is to set the viewport with MinDepth = MaxDepth = 1.0f, and use a rasterizer state with DepthClipEnable set to FALSE.