All apps wiped from jailbroken iPhone (iOS 7.0.4) after reboot from battery loss

It's a bug. Your apps aren't gone but just not visible on your Home Screen.

To restore them, reinstall a package through Cydia (either an existing one, or a new one will suffice). Then either respring (can be achieved via WinterBoard) or reboot your device (unnecessary if you reinstall a package that requires SpringBoard to restart, like ClassicDock for example).

I have unfortunately not been able to pin down the exact cause of this.

This is the third time I've had this issue: the very first time I ended up restoring my iPad. The second time it happened I ended up re-downloading all the apps but noticed that the apps that were in the folders were getting downloaded but also re-creating the same folders that they were in and going in there.

I now found I solution:

1. Download iFile from Cydia
2. Navigate to /var/mobile/Library/Caches and delete com.apple.mobile.installation.plist
3. Shutdown the iPad by holding down the power button and then swiping it to power off
4. Reboot *If deleting that file did not work, try also deleting 'com.apple.mobile.installation_backup.plist'*

This method is the fastest way to restore the missing apps. It restores also the data in those apps. Note: (the folders will not be restored only the apps). It works only if you lost your apps during reboot/restart (bug).