How To Sync (iDevice to iTunes)

Step 1:

Get AppSync for OS 3.1 (3.0 if you’re not on OS 3.1.*) or Installd Patch (if you’re not using a 3GS) from Cydia. You can get them by adding or respectively to Cydia and searching for them. Use only one of them. Do not get both. Read: Explained: Patching The Installd.

Step 2:

Enable iTunes Sync in Install0us under Settings.

Step 3:

Go to Preferences in iTunes and head to the Devices tab. Check the box to prevent automatic syncing upon device plug in. You can uncheck this after you’ve succeeded at Step 5.

Step 4:

Plug in your iDevice and right click on its name listed under Devices in your iTunes sidebar on the left. Select Reset Warnings. You can also do a global reset (i.e., not device-specific) via the Advanced tab in Preferences as shown in this image.

Step 5:

Click on Sync (as shown in this image OR you can click on the Sync shown in step 4’s screenshot) and you will receive the above dialogue box asking you to transfer purchases. Do not check the “Do not ask me again” box because regardless of your input this time, iTunes will take “do not transfer” as the default action.

If the dialogue box in Step 5 does not show up, or it doesn’t transfer even though you told it to, go to Step 4 and click on Transfer Purchases (as shown in this image). Keep doing it until it doesn’t detect anymore apps to transfer.

Last resort:
If everything still doesn’t work, you’re SOL. As a last resort, uncheck Automatic Delete in Install0us as shown in Step 2’s screenshot. Before plugging in your device, SSH the .ipa files to your computer (or any form of wireless transfer), then drag and drop them anywhere onto iTunes’s interface. iTunes does not reject cracked apps that are added this way; it will add them to the Applications Library. Once the apps are there you can safely sync as they won’t be deleted from either iTunes or your device, at least until user input.