If you have iFile installed try this, it will reset cydia and if you restart afterwards will take you to the first screen in cydia, it will leave your apps installed.
Navigate to /private/etc/apt/sources.list.d
Delete the file "cydia.list"
Navigate to /var/lib/apt/lists
Delete all of the files in this folder except the one called "lock"
Navigate to /var/lib/apt/lists/partial
Delete all of the files in this folder
Navigate to /var/lib/cydia
Delete the file "metadata.plist"
Alternatively, if ifile is not installed download ifunbox (mac or win) and acces your iphone file structure from your mac/pc