I have been meaning to try and find a way. Let me play with CWM and maybe Titanium Backup. There may be a way to backup aps, then flash new firmware, then restore aps. The problems is, some of your games may be configured to the stock rom. You have to keep in mind that some of those options for Titanium may be on pro version too, dunno.
But as far as apps and games and all that, Yes you will have to start over if you use the Batch tool method.
And as far as the update.img method, it's a toss up whether it's ganna work or not.