I don't believe NHibernate would be able to compile both together to create a singular mapping. If the goal is to use a different set of mappings in one app versus another, you need to simply create two different mappings. If the goal is to have subclasses, there is a SubclassMapping interface you can extend.
Edit:
In looking over my notes, an extension to my answer about creating a different set of mappings would be the case where you have some feature plugged into your app that needs a different (sometimes more, sometimes less involved) mapping. To do this you need to have NHibernate generate them separately and add them to the configuration separately. Using conventions, this creates two separate sets of mappings (which contain some overlapping, but differently mapped, entites) that are plugged into one configuration:
NHibernateConfiguration.BeforeBindMapping += (sender, args) => args.Mapping.autoimport = false;
var pluginMappings = new PluginMapper().Mappings;
foreach (var hbmMapping in pluginMappings)
NHibernateConfiguration.AddDeserializedMapping(hbmMapping, "PluginModel");
var mainAppMappings = new AppMapper().Mappings;
foreach (var hbmMapping in mainAppMappings)
NHibernateConfiguration.AddDeserializedMapping(hbmMapping, "AppModel");