Foreflight has issued some cautions (http://blog.foreflight.com/2011/10/14/flying-with-foreflight-and-ios-5/) about using the new IOS5 on your iPad or iPhone.
It seems the new version can remove app data from your device if disk space gets low. You have no control over what gets removed so there is the potential to lose charts or flight plan data. The best way to avoid this is to make sure you have some extra space on your mobile device. More details and tips are in the ForeFlight blog post.
Even if you don’t use ForeFlight, the information will be useful to any iPhone or iPad user.
Sources with knowledge of this issue say Apple is working on an update to IOS5 that will address the deleted data problem. Watch for version 5.0.1 to be released soon. Updates from the major aviation apps should follow soon after.