Apps missing after sd card unmount
This sounds like a case of a vital hidden folder that you're missing - when apps are moved to the SD-Card, a hidden folder called .android_secure is created which is where the apps are stored in!

This is a common mistake to make, when replacing a SD-Card for a bigger one, so the moral is to ensure, when transferring to a bigger SD-Card, do not forget the hidden directories including .android_secure. Upon restart after inserting the bigger SD-Card, Android will re-scan the card and proceed to look in that specific hidden folder, for any apps that are moved to external storage and loads/caches the shortcuts for those respective apps.