Application Identifier Entitlement Value has Changed?
Have you transferred the app from another developer account to your one? The previous provisioning ID will obviously be different.
UPDATE - For clarification
I have noticed that this answer is getting a lot of views so I will just edit it to include my further explanation from the comments below.
Basically the previous version of your application will NO longer be able to access keychain in order to save secure strings such as passwords (if it contains this functionality). This is because the distribution/provisioning profile it was signed with contains a different ID than the one you are using in your new distribution/provisioning profile because you have transferred your app from a previous account to your new one.
However any NEW versions of your app which are signed with the latest distribution/provisioning profile WILL be able to access keychain as normal in order to save secure data if they need this functionality because they are signed with a distribution/provisioning profile which contains the latest App ID for that app.
The warning informs you that your updated app will not be able to access items previously saved in the keychain. The old version of your app can still access and store items in the keychain, just like the new version. However the two versions cannot share information in the keychain.
In summary, all data saved in the keychain will be lost once a user updates to the new version. All information stored in UIPasteboard will also be lost.
You can see this message if:
The app was transferred to your account and you are updating it for the first time. In this case there is nothing you can do to prevent the warning (and side effects).
Your app was added to iTunes Connect before June 2011 and you recently updated the provisioning profile used by the app. Either your old provisioning profile was using a wildcard (*) App ID and the new one is now using a specific App ID, or the opposite (less likely). In the later case you can switch back and avoid the warning (choose the correct provisioning profile in Xcode). In the other case, chances are your app needs access to services like Game Center, Push Notifications (or anything that a wildcard App ID will not let you use) and you cannot avoid the warning.
If you want more details, the warning is related to the fact that App ID prefixes are attributed by Apple and cannot be changed. Check the "App IDs" section in Apple's "Certificate, Identifiers & Profiles" page (https://developer.apple.com/account/ios/identifiers/bundle/bundleList.action - you need to sign in), press on an ID and look at the "Prefix" field. You can also check Apple's Technical Note 2311 https://developer.apple.com/library/ios/technotes/tn2311/_index.html
Lastly, you might thing you could avoid the warning by changing the Keychain Access Groups (keychain-access-groups) field of your provisioning profile. This will not work as Apple will not let you have different prefixes for the App ID and for the Keychain Access Groups.
As of the stricter security in iOS 8.1.3, this is much more serious than the warning suggests; see https://developer.apple.com/library/ios/technotes/tn2319/_index.html#//apple_ref/doc/uid/DTS40013778-CH1-ERRORMESSAGES-UPGRADE_S_APPLICATION_IDENTIFIER_DOES_NOT_MATCH_THE_INSTALLED_APP. It seems like the mismatch causes a failure to upgrade to the new version. When I try to update via Xcode, it fails with an error to the device console like that in the Tech Note: “Upgrade's application-identifier entitlement string [....] does not match installed application's application-identifier string [....]; rejecting upgrade.” Trying to update via iTunes seems to fail silently.
I hope that the answer is simply “this error is simply an indication that Xcode has chosen the wrong provisioning profile,” verified as in https://developer.apple.com/library/ios/technotes/tn2318/_index.html#//apple_ref/doc/uid/DTS40013777-CH1-TNTAG65. But I last submitted my app many Xcode versions ago, and finding the right one may be a challenge.
Note the phrasing “Xcode has chosen the wrong provisioning profile”; to make sure that it chose the profile you thought you chose, click on the arrow next to the chosen profile’s truncated name in the archive verification dialog. To double-check this, submit to the App Store with a known error (I inadvertently used a missing icon), so that you see whether the warning appears.