Hello Ryan,
You can duplicate the chunk in the same project workspace and work with each chunk independently, as with different projects.
In case you want to preserve the alignment results and experiment only with the further processing steps (building point cloud, model, DEM, orthomosaic, etc), then you can work in the same chunk: uncheck "set as default" option from the context menu of the corresponding asset in the workspace pane and then build the new asset of the same type. Thus you can have multiple point clouds, elevation models, orthomosaics in the same chunk, based on the same alignment.