Most apps have flags to be used to preserve xattrs. Others were written as though they never knew xattr existed and therefore fail to use the kernel flags to preserve them. But it is not that difficult to preserve them once you are using them.
I use rsync to back up my book, music, and video collections (which is where I use them) and the meta data is backed up with them - so if something ever happens I can always restore them. The xattr commands also have a backup and restore for just the xattr built in.
