When you upgrade to 4.1 it will remove the jailbreak and cause you to lose everything the JB had. Then you have to JB again for 4.1
I have PKG Backup up so my hopes are if I make a backup right now and save the backup onto my PC as added safety, I can update to 4.1, jailbreak with Limera1n or Greenpois1n when it comes out, put back Cydia, re-download PkgBackup, and restore from my backup bringing back everything I had. I'm not ready to upgrade yet but I'll find out eventually.