If the message does not go away there are a couple things you can try. A local copy is stored on your device so as long as you don't delete the app you should be able to retrieve your game. If you have Pocket Planes installed on multiple devices, you can delete the app from all but one device (the one with the highest level) and then reinstall once it is working again. Only try the follow solutions on one device at a time. Ensure that you have a good internet connection and please try the following:
Disabling syncing then go into Menu -> Settings and re-enable iCloud Syncing. Close Pocket Planes and wait a couple seconds, reopen the game and the message should go away.
Another way to kick start the sync is to logout and back into your iCloud account. From an iPhone/iPod or iPad, go into Settings app on your device and into the iCloud settings. Scroll to the bottom and tap the red "Delete Account" button which will sign you out of iCloud. Then sign back in using the same account. This does not delete your iCloud account of content from the cloud, it just removes it from your current device and is restored when you log back in. Some players have reported that this does not work the first time and that after the 2nd or 3rd time of deleting and logging back in the problem is resolved.
Finally if none of these work, you can disable iCloud syncing for Pocket Planes and play the game on one device. Just disable iCloud syncing in the app settings or as instructed above.
Note, Pocket Planes only uses iCloud for syncing between devices and does not maintain a backup of your game once deleted from all devices. If you've deleted the app from all of your devices you will need to rely on a recent iTunes or iCloud device backup for restoring your game. Please see the following link for more info on backing up and restoring: http://support.apple.com/kb/ht1766
Mac users, iCloud syncing for the Pocket Planes Mac version is no longer supported.