I've created alerts on some scrips using Google Data. Now for some reason, I switched to Yahoo Data. The alerts created earlier were there but not visible in the Portfolios and  Watchlists Screen. Now I've to create them again for all stocks in order to be visible in Portfolios and Watchlists Screen.

Unfortunately scrip names of Yahoo and Google don't match. They match only for US and Canada stocks. For rest of the world they differ too much to make them source independent.
In your case to switch from Google to yahoo you can open alert_repo.xml in notepad and replace 'Google' by 'Yahoo!'.
But before you do this you should take backup of the file.  :)

Note: You can type %appdata%\Lunetek\Stockalyze in Run window to go to the directory where you can find the file I talked about.