The safest and easiest way I have found, that completely backs everything up, and also restores everything (including the database) is to follow the procedure below.
This is not the most efficient method, and there is downtime of Alfresco during the backup, but your restore WILL work.
To back it up:
1. Stop Alfresco, and the database (Postgres). This is a cold backup.
2. Copy the entire Alfresco directory (tar it up with linux, or copy and zip it up in Windows) to another directory.
3. Start Alfresco and the database again, so you can start using Alfresco again.
To restore:
1. Stop Alfresco, and the database (Postgres).
2. Delete the the current Alfresco directory (MAKE SURE YOU HAVE A COPY FIRST)
3. Copy the backup Alfresco directory to the original Alfresco location.
4. Start Alfresco and the database.
I have done this on both Windows and linux Alfresco servers and successfully restored several times this way.
Hopefully, an Alfresco employee will answer your post here, with another suggestion, if this simple method doesn't meet your needs.
If you need to do a "hot" backup, you will need to follow a more involved process.