First off I'm going to presume that you've installed 6.2
When you did that, did you have the installer install the servers.ini file, and did you tell it to overwrite your current file?
If so, your server.ini file has not been lost. It is available in the backup directory (for Windows XP, default location) C:\Program Files\mIRC\backup
If you didn't do the above, then I'm not sure what happened.
I'm also not sure what comes in the default servers.ini file with 6.2, as I didn't have my current setting overridden by the new files.