Your apps are the least of your worries right now, getting your phone booting should be your main concern. You're gonna need to start fresh anyway, attempting to dirty flash after such a fatal mistake is an awful idea. So yes, you're gonna lose your apps, because you need to perform a full wipe (system/data/cache/dalvik cache) and clean flash a ROM to get your phone booting. Don't you make backups of your apps with Titanium anyway?
Sent from my Evita