The iPhone Backup Extractor extracts data from iPhone backups, from iCloud backups, and from other iCloud data. As such, so long as the last backup was taken before the data was deleted, it will recover your information automatically. However, if the data was deleted before your backup was taken, it makes sense that the backup won't contain your data.
Fortunately, Apple don't purge deleted data from their database files, so it is often possible to recover deleted data, even from before a backup was taken. This works particularly well for iMessage, SMS, WhatsApp, note and contact data. (By extracting the SQLite databases from your backup in Expert mode, and opening them in Notepad, you should see fragments of any data that has been deleted.)
How does recovery of deleted iOS data work?
Reincubate iPhone Backup Extractor has a sophisticated version of this technique integrated with it, saving the need for any forensic recovery process. Our implementation outperforms all of the dedicated SQLite recovery tools we've benchmarked it against.
In addition to this, there are other techniques that we use in the application, and that our support team are able to assist with. One of those involves examining iCloud backup snapshots, which can prove fruitful for recovery of iOS data, and iPhone Backup Extractor can fetch those snapshots for you.