MISSING PACKAGES AFTER UPGRADE/RESTORE TO 7.0.6 FIX
This topic recently came up in #iphonedev on irc.saurik.com. I speculated that Cydia's cache got out of whack with the state of the packages that the underlying package manager (apt) knew about. The procedure to correct this is straightforward but will require you to tinker with some of the files the Cydia stores on your iOS device.
I recommended the following steps, and it seems to have helped Tatsh.
Cydia stores the "Release" files (the repository package lists) in /var/lib/apt/lists
Make sure Cydia is closed
You need to delete all files with the following TWO exceptions: lock (file) and partial (directory).
Once the files are deleted, re-open Cydia.
Cydia will then re-download all of the Release files from the various repositories
When it says "reloading data", Cydia is resolving the packages from the repositories with the underlying package manager (apt)
After this step is performed, your package cache will be consistent again
So, how do we delete these files?
The easiest way is to download the iFile package (if it shows up in Cydia). It's shareware and will let you use it for a limited time. I recommend you purchase it, because it's a great tool to have. Navigate the filesystem to the /var -> lib -> apt -> lists directory. Use the edit button in the upper right to allow you to select the files. Remember, do NOT select lock nor partial. Once the files are selected, tap the trash can icon in tab bar. Empty the trash. Fire up Cydia and get back to work.