I upgraded my iphone from software version 3.1.2 to 3.1.3 and it locked my phone up and removed all of my apps from cydia rock and blackra1n. is it fixable? can I unlock my iphone again?

Step 1: Update iTunes to the latest version available and reboot your computer.
Step 2: Download BlackRa1n from our iPhone downloads page and install it, then reboot your PC (note that rebooting is not necessary but I always do this as a precaution).
Step 3: Plug your iPhone to your computer and launch BlackRa1n. Click on “make it ra1n”.
Step 4: Your iPhone will now enter recovery mode. The regular recovery mode image on your iPhone will be replaced by a picture of GeoHot.
Step 5: BlackRa1n will run on your iPhone and then it will reboot.
A pop up will show up asking you to donate. If you successfully jailbreak your iPhone, I suggest you send $5 or $10 to GeoHot.
Step 6: Once your iPhone reboots, you will notice a new icon on your springboard. This is BlackRa1n. Now make sure you have internet connection and launch BlackRa1n on your iPhone.
Step 7: Choose what installer applications you want to install on your iPhone and then tap “Install”. I suggest only installing Cydia but you may install them all if you want to.
BlackRa1n will download and install the selected applications.
Step 8: Once done installing, your iPhone will respring and you should see your installer app on your springboard.
Step 9: Once your installer app (Cydia in our case) is installed. You can safely uninstall BlackRa1n by launching the app and selecting “uninstall balckra1n”.
Step 10: Reboot your iPhone. You’re done!

First of all, you'll need an iPhone 3GS (of course). This trick works for the version 3.1.2 of Apple's firmware. First, you'll need to jailbreak your iPhone 3GS. For that, you'll need to download the blackra1n.exe application from this website: www.blackra1n.com, then you'll need to run the application (nothing complex, just a one-button-easy-process) and wait for your iPhone to reboot (note that after this you won't be able to shutdown your iPhone again, as this is a tethered jailbreak, if you do, it'll restart in restore mode and you'll need to manually boot it again with the blackra1n program). When the jailbreak is done, you'll see a black-drop-shaped icon in the application list on your iPhone, tap it and install the cydia and Rock applications. When you finish installign those, tap the Rock application and then tap on "manage" at the right bottom of your screen. After that, tap "Manage Sources", then "Edit" (top-right of the screen), then "Add" (Top-left), then type exactly this: "http://sinfuliphonerepo.com" (without the quotes). Now, after confirmation, still in Manage>Sources, scroll down until you see a section called "User entered". Tap the arrow to show a list of applications. The first one should be an application called "3G Unrestrictor", install it. After installed, open the application from your springboard and select these application if you have them: Skype, Nibuzz, App Store (Choosing it also unlocks iTunes Store) and any other application that doesn't allow a certain type of connection over the 3G network system. And as a bonus, you might grab some other free applications for your iPhone, such as old game consoles emulators, file managers (iFile Cracked) and more!

There's tons of information available on the internet on how to jailbreak your iPhone. That's the positive, and that's the negative too! You get stuck with questions like "will this method work?", "how is method 2 different from 1,2,..1000?" and so on! I thought I'd make things a little simpler by giving you a method that worked for me, and a lot of my friends on both 3G and 3GS models. So here we go:
Step 1: Preparing your iPhone.Restore your iPhone by connecting it to iTunes. Download and install the latest version of the OS 3.1.2 (as of now).
Step 2: Get iTunes out of the way!
End the process "iTunes helper" from the Task Manager (Windows) or Activity Monitor (Mac)
Step 3: Download the Blackra1n software here: http://www.blogsdna.com/5465/download-blackra1n-rc3-to-jailbreak-unlock-iphone-3g3gs-3-1-2.htm
Step 4: Run Blackra1n and let it do it's thing!iPhone will restart now.
Step 5: Disconnect your iPhone from computer, and look for an app named "blackra1n" in the phone. Open it, and install the packages listed in the app: Cydia, Rock and Sn0w.
Step 6: Restart phone
Insert your new sim and enjoy your jailbroken iPhone 3GS!
For more information, visit: http://dontwannaluv.blogspot.com.