How can I update a specific layer of a multilayer exr file? Is it possible to "update" parts of a multilayer exr while retaining other render layers?

Let's say I have two layers A and B. I render both layers to the same exr and later I decide to re-render layer B (with option "Only render the active layer" checked). When I click on "Animate", Blender overwrites all existing exr files, so layer A is lost. I don't want to re-render all layers, since it's pretty time-consuming.

Do I have to use multiple exr files - one for each layer - to fix this? What's the benefit of the multilayer exr then?
You do need to render out a new OpenEXR file.

Bring the OpenEXR files you already rendered into the compositor using an image sequence node. Then add a file output node and set it to OpenEXR multilayer. Reroute the outputs to combine the images as needed and re-render the sequence.



The basic procedure to setup the OpenEXR layers is outlined on this post:Combining .exr files?



You might need to render out a set of dummy files to automate the rendering.
See this post:Export multi-pass .exr image sequence from cycles?