iOS 5.0.1 and iWork apps
As is well documented in these support pages, the best way to make iCloud sync your iWork apps across all devices and iCloud.com is to ensure you have set the "Documents and Data" setting to "OFF" (this is in Settings>iCloud); then ensure that the relevant app is set to "Use iCloud" (this is in Settings>APP).
As soon as I updated to iOS 5.0.1, ALL my documents in the apps disappeared but they can still be seen at iCloud.com; after further experimentation I can now report that if I leave my settings on my devices alone, then any document I bring into the app will still sync to the other devices. For example, if I bring a Pages document into my Pages app on my iPhone, then my IPad receives the same (edited) document a few seconds later.
The problem appears to be with iCloud.com as any files I drag into the iWork section of the site refuse to:
a) sync with the iOS devices and
b) download back to my mac
It seems that Apple MAY have ironed out a few bugs within the iOS but still have a lot of work to do with iCloud.com
In summary, I have found that after, "upgrading" to iOS 5.0.1, there is no need to change any settings on the devices. You need to work around the iCloud.com issue. To protect your files, keep copies of them on your MacBook/PC before transferring them to your iOS devices. I am transferring files using the File Sharing section of iTunes and I am using Dropbox too. The latter means I can be sure I have copies I can access anytime.
Having to find a workaround is not what I expect from Apple; you are letting your loyal fans down and I can only say I am for the first time ever, very, very disappointed in you
SK
iPad, iOS 5.0.1