How to stop syncing apps with iTunes without wiping them from my iPhone?

Is there a way I can stop syncing apps with iTunes without first obliterating the apps from the iPhone and re-downloading them?

Now that iOS 5 and iCloud are released, I want to stop storing all my apps on my computer, and instead just let them be downloaded directly to each of my devices. Music, podcasts, etc. should still sync with my computer.

However, when I deselect "Sync Apps" in iTunes, I get the message:

Are you sure you do not want to sync apps? All existing apps and their data on the iPhone "myPhone 4" will be removed.

It seems like an awful waste of time and bandwidth to force the phone to redownload all my apps just to tell iTunes to stop syncing them.

From testing, it seems you can't break that link without having to re-download. Since the change requires you to synchronize the phone, you will need to re-download the files from the phone once you've un-ticked the box, since the synchronize does remove the applications completely.

Unfortunately the answer to your question is right now there isn't a default way, but I suspect it will become possible in future iTunes versions.

I have looked for possible hacks to do this and have yet to find one that doesn't require jail breaking to copy the files back.

What worked for me was to setup my device for wifi sync first. Make sure under the edit menu and preferences / devices (this is important) that you have it set to prevent automatic sync. Right click on the device in the left pane of itunes and reset all warnings. Have the cable disconnected but the device still visible via wifi. Uncheck sync apps, then ok the warning about removing the apps from the device. Then click "summary" and uncheck sync over wifi then apply in the lower right.

Now reconnect via cable turn wifi sync back on and sync your device via wifi or cable doesn't matter which. Now disconnect the cable, goto apps in iTunes and delete all apps. Ok the warning about removing the apps from the device. Goto summary and uncheck sync via wifi and click apply in the lower right. Then you can reconnect with your usb cable and turn on sync via wifi again.

At this point a popup will tell you that there are apps that you need to transfer to iTunes or they will be removed from your device. Check don't show this again and then click don't transfer. Now you can go into edit and preferences under General and uncheck apps altogether if you want the iTunes apps folder to go away as well.

I did this with both my iPhone and iPad2 and I still have my apps on them.

Good Luck.