Ok guys I found the answer !
I simply needed to use the ImportApplicationInfo param while deploying the new application
Here's the code for those who wants :
//Set connection properties required to invoke LiveCycle ES2
Properties ConnectionProps = new Properties();
ConnectionProps.setProperty(ServiceClientFactoryProperties.DSC_DEFAULT_EJB_ENDPOINT, "YOUR_ENDPOINT");
ConnectionProps.setProperty(ServiceClientFactoryProperties.DSC_TRANSPORT_PROTOCOL,ServiceClientFactoryProperties.DSC_EJB_PROTOCOL);
ConnectionProps.setProperty(ServiceClientFactoryProperties.DSC_SERVER_TYPE, "WebLogic");
ConnectionProps.setProperty(ServiceClientFactoryProperties.DSC_CREDENTIAL_USERNAME, "administrator");
ConnectionProps.setProperty(ServiceClientFactoryProperties.DSC_CREDENTIAL_PASSWORD, "password");
//Create a ServiceClientFactory object
ServiceClientFactory myFactory = ServiceClientFactory.createInstance(ConnectionProps);
ServiceRegistryClient serviceReg = new ServiceRegistryClient(myFactory);
// Get conf file
FileInputStream fileAppInfo = new FileInputStream("d:/LCConf.xml");
Document appInfo = new Document(fileAppInfo);
// Get LCA file
FileInputStream fileApp = new FileInputStream("d:/test.lca");
Document lca = new Document(fileApp);
// Deploy using the xml and the lca
ApplicationManager appManager = new ApplicationManager(myFactory);
ImportApplicationInfo appInfoSettings = new ImportApplicationInfo(true, appInfo);
ApplicationStatus appStatus = appManager.importApplicationArchive(lca, appInfoSettings);
System.out.println("Returned code : " + appStatus.getStatusCode()); // 1 is success