You should rarely modify the configuration of a search collection after it has been created, for reasons such as the following:
To eliminate or minimize the need to programmatically reconfigure existing collections, it is a good idea to maintain some number of correctly-configured search collections that you can use as a starting point for any new collection that you create programmatically, as discussed in Creating a Search Collection.
If you have access to the Watson Explorer Engine administration tool, that tool is designed to simplify modifying collections, restarting crawls, and so on. However, should you need to programmatically modify an existing collection, the next few sections explain how to retrieve current configuration information, modify that information, and write your configuration changes back to the collection.