All the commands are
here. Here's how it works - Android will look in three places for apps:
/system/app
/data/app
/data/app-secure
/system/app is system apps that come with the phone or ROM. A2sd does absolutely nothing with these. These apps cannot be uninstalled (or pushed here) unless you have root. /data/app and /data/app-secure, however, is where the system will look for all your normal apps. As far as the system is concerned, all your apps are still there even after you have moved them with a2sd. A2sd does this by moving all your apps to the ext partition, which is mounted at /system/sd. When you go to the /system/sd directory, you're looking on the ext partition on your sdcard. If you go look now, you'll see app and app-secure directories. Inside those are your apps. The system knows they exist because a symlink (Linux terms for a shortcut) has been created that redirects from /data/app and /data/app-secure to /system/sd/app and /system/sd/app-secure. The same thing will happen if you move dalvik cache to the sdcard. The command is a2sd cachesd. That will move dalvik cache to the sdcard using the same method.
Now that we know that was the problem, you can probably get away with doing something like this if you want to keep your previous setup:
1) Wipe data/cache/dalvik/sd-ext
1) Restore previous nandroid backup
2) Wipe cache/davlik cache (don't wipe data)
3) Reflash ROM and whatever mods you want
4) Rerun a2sd commands to move apps to sdcard
I can't promise that will work, but it should be fine.