To reproduce:
1. Open attached project. It has a texture that is set to be in an asset bundle with a variant (high). There is also a material that references the texture - it is set to be in an asset bundle without a variant
2. Open scene "test"
3. Enter play mode - the asset bundles are loaded and the material is applied on a sphere
4. Click the sphere and expand it's material - notice that the texture is 'none'. The reference has been lost.

The same issue happens if the material is in an asset bundle with a variant while the texture is in a bundle without a variant.

The issue does not happen if both asset bundles don't have a variant or both have a variant.