I have tried the following code to update the custom fields context.
CustomField field = customFieldManager.getCustomFieldObjectsByName(customField).iterator().next();
FieldConfigScheme defaultConfig = field.getConfigurationSchemes().iterator().next();
List<JiraContextNode> contexts = defaultConfig.getContexts();
List<JiraContextNode> newContexts = new ArrayList<>(contexts);
newContexts.add(projectContext);
FieldConfigSchemeManager fieldConfigSchemeManager = ComponentAccessor.getFieldConfigSchemeManager();
fieldConfigSchemeManager.updateFieldConfigScheme(defaultConfig, newContexts, field);
ComponentAccessor.getFieldManager().refresh();
But the new context does not get applied .