Using J-link to Register Server

I don't think that this is a good idea. So for multiple reasons a server change with all backgroundjobs could get you some mess inside the data directories.

Anyway, if you want to do it it's straight forward:

String pdmServerData = "Name;;;URL;;;USERNAME;;;PASSWORD;;;WORKSPACE"

String[] psd = pdmServerData.split(";;;"); //NOI18N

boolean mknew = true;
Servers servers = session.ListServers();
if (servers != null) {
String servername = psd[0];
for (int i = 0; i < servers.getarraysize(); i++) {
if (servername.equals(servers.get(i).GetAlias().toLowerCase())) {
mknew = false;
servers.get(i).Activate();
}
}
}
if (mknew) {
session.RegisterServer(psd[0], psd[1], pdmServer.charAt(2) == '1' ? psd[4] : null);
}

I do ours with a trail file. There is a batch file that builds the user environment (pulls configs, .psf, start parts, material, etc to the local machine from the network) then check to see if a server is registerd. If there is no registered server it runs a trail file that gets you to the point of logging into windchill, so it populates the server name box, etc.

Echo Launching Pro/E
	IF exist "%PTC_WF_ROOT%\.Settings\config.fld" (
		START "" "%DIR_PROE_BIN%\parametric.exe"
	) ELSE (
		XCOPY "%DIR_PROE_CONFIG_BIN%\registerserver.txt" "%DIR_PROE_DATA%\" /Q /R /H /I /Y
		"%DIR_PROE_BIN%\parametric.exe" "%DIR_PROE_DATA%\registerserver.txt"
	

Here is what I ultimatly went with. Seems to work pretty well. 
Thanks to @Eike_Hauptmann and @jmikesell for helping out.

public String isConnected(){
		try {
			Server activeServer = session.GetActiveServer();
			printLog("isConnected: " + activeServer);
			String severList ="";
			Servers servers =null;
			servers = session.ListServers();
			//printLog("isConnected: number of Registered Servers Found = " + servers.getarraysize());
			if(servers != null){
				for(int i=0; i<servers.getarraysize(); i++){
					Server server = (Server) servers.get(i);
					String serverName = server.GetAlias();
					printLog("isConnected: Server name: " + serverName);
					serverName += serverName;
					severList = serverName;
				}
			}
			if(!severList.contains("pdm.server.com")){
				printLog("isConnected: Production Server Not Found ");	
				String macro = "";
				printLog("RegServer Macro: Start");
				macro += "~ Command `ProCmdUtilWebRegServ`;";
				macro += "~ Select `siteregistrydialog` `MenuBar1`1 `ServerMenuPane`;";
				macro += "~ Close `siteregistrydialog` `MenuBar1`;";
				macro += "~ Activate `siteregistrydialog` `ServerRegisterNewPshBtn`;";
				macro += "~ Input `registernewserverdlg` `NewServerNameIPanel` `pdm.server.com`;";
				macro += "~ Update `registernewserverdlg` `NewServerNameIPanel` `pdm.server.com`;";
				macro += "~ FocusOut `registernewserverdlg` `NewServerNameIPanel`;";
				macro += "~ Input `registernewserverdlg` `NewServerLocationIPanel` `http://pdm.server.com/Windchill`;";
				macro += "~ Update `registernewserverdlg` `NewServerLocationIPanel` `http://pdm.server.com//Windchill`;";
				macro += "~ FocusOut `registernewserverdlg` `NewServerLocationIPanel`;";
				macro += "~ Activate `registernewserverdlg` `NewServerCheckPshBtn`;";
				session.RunMacro(macro);					
				return "Yes";					
			}else{
				printLog("isConnected: Production Server Found ");
				return "";
			}

		}catch(Exception e){
			StringWriter sw = new StringWriter();
			e.printStackTrace(new PrintWriter(sw));
			printLog("isConnected: " + sw.toString());
		}
		return"";
	}