If storage space on an iOS device is tight, the software will clear out the tmp and Caches directories to create more room.
Ament explained that app developers have used those directories to store certain files - Instapaper, for example, stored downloaded articles in those locations - since these two directories do not get backed up when a devices is synced with iTunes. It was a way for developers to speed up the backup process by selecting less important files to be stored in those two locations.
According to Ament, "full restores" don't happen enough to have justified all files to be located in the app folder and the usage of tmp and Caches was a good compromise. Apparently many app developers are using this approach. In fact, Apple is asking app developers to store non-user generated, "re-downloadable" files in the Caches folder for iOS. However, it is this exact folder that gets cleaned out when iOS sees the device running low on space.
For developers, that means that Apple has eliminated a space that can safely store app data that do not need be included in a backup. From Apple's perspective, that may be not so much a problem as re-downloadable data can be easily deleted and replaced per user demand. However, it could be a problem for a user who may, as Ament calls, it stocks up on pages to read before a flight - perhaps to a different country.
Getting those pages back is possible, as long as there is a wireless connection, but even if that connection is available, you may incur roaming charges to re-download the content.