Syncing apps before 401 upgrade

Hi,
I've purchased loads of apps via the app store on my phone and have it set up how I like it. When I connect to iTunes it asks me if I want to install ISO401 and warns me to back up my apps - sound advice.
When I go to the apps tab in for my phone in iTunes on my PC and select "sync apps" it warns me "are you sure - all existing apps and their data on the iphone will be replaced by apps from this iTunes library".
Does this mean the apps I have downloaded directly onto the phone will be lost? Some of these are huge downloads, I don't want to have to do them again. And I don't want to have to mess around with setting up all the data again.
Help.

Every time you sync they should be getting synced to your computer. You should also ensure you are logged into the iTunes store on your computer so it knows your account info to match to what was used on phone when you downloaded them direct (this normally isn't issue as default is iTunes keeps you logged into store).
But try the Transfer Purchased Content from File menu before syncing and see what it does.

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