Syncing Apps from Iphone to Itunes and vice versa, quick question.

Hello, so I had a small question to ask about transferring apps from both the iphone to itunes.
Basically, I downloaded an app from the app store ON my iphone.
I've made a lot of progress and have a lot of data in this app.
The(Sync app) box was never checked on my itunes, so I transferred my purchases from my iphone to my itunes, and now i've downloaded a few more apps (over 20mb) ON itunes that I want to put on my iphone.
Thing is, when I click "sync apps" it gives me a warning saying something along the lines of "Apps in itunes will replace all in iphone, including data"
Now, i've already transferred my purchases, so all the apps from my phone are on itunes, but if I sync, will I lose the DATA in my apps on my iphone? Or will the data remain in those apps?
Basically, will syncing my apps replace my settings/data/progress of the apps I have on my iphone?

There is no data in the apps themselves. Your app data is stored in the backup file iTunes creates. http://support.apple.com/kb/HT1766
From Page 179 of http://manuals.info.apple.com/enUS/iphone_userguide.pdf, "You can reinstall an app and restore its data as long as you backed up iPhone with iTunes on your computer. (If you try to delete an app that hasn’t been backed up to your computer, an alert appears.) To retrieve the app data, you must restore iPhone from a backup containing the data."
So, make a backup before you click the "Sync apps button. Then, you may have to restore your phone from that backup to reload the data.

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I've transferred my apps from the iPhone to iTunes by clicking on "Transfer Purchases" That's all good so now they both have the same apps.
I've installed the latest ver of iTunes so ultimately it allows us to re-arrange the pages of apps on the iPhone through iTunes.
When the checkbox "Sync Applications" is unchecked I can see my apps as arranged on the iPhone, when I check it everything is different. That's not what I want as it tells me my settings will be copied from iTunes to iPhone.
What I want is for it to recognise my latest apps setup on my iPhone and THEN allow me to re-arrange it from iTunes before syncing.
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Message was edited by: mudbucket

As already mentioned, you can only sync to one computer at a time. To be able to go back to your computer, disable autosync in itunes, connect your phone and right click on it in the device list and choose Backup. Transfer your purchases the same way after that. Then sync your phone. All media content will be erased during this process, but you can restore your phone from the manual backup you made before. See also: "About backups": http://support.apple.com/kb/HT1766 and "Restoring" : http://support.apple.com/kb/HT1414

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How can you retain the app folder structure you have painstakingly created on your iPhone (OS4.3) when syncing apps with iTunes?
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Thanks Mr. Gnome I was aware of that - it was a rhetorical question as far as Apple are concerned, but I do hope someone out there may have found a way around this illogical glitch.
By the way, I think you meant your link to be...
http://www.apple.com/feedback

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I have close to 200 apps on my iPhone structured into approx 50 folders.
These apps are downloaded firectly from iTunes (via wifi).
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I used the option "Transfer purchases" for that.
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I have right-clicked on my device and selected "transfer purchases," but when I checkmark "sync apps," I still get that annoying "are you sure you want to sync apps? ..." warning.
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are you positive,
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iTunes cannot sync... apps not determined installed on...: Apple Support Communities
installed apps could not be determined...: Apple Support Communities
not determined

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