I was wondering if the folder alf_data/backup-lucene-indexes is a mirror of the folder alf_data/lucene-indexes Because, I reindexed all so alf_data/lucene-indexes is healthy, and alf_data/backup-lucene-indexes contains some errors I know. Will the backup process will OVERWRITE all alf_data/backup-lucene-indexes with folder alf_data/lucene-indexes ?
The alf_data/backup-lucene-indexes folder is recreated automatically every night by copying alf_data/lucene-indexes directory in its entirety. The only reason it exists is to support hot backup - Lucene does not cope well with concurrent access to its persisted files, so to support hot backup Alfresco (safely) duplicates alf_data/lucene-indexes, then the backup process must backup only the copy.
If you're performing cold backups exclusively, you need only backup alf_data/lucene-indexes - in fact you could shut off creation of alf_data/backup-lucene-indexes altogether, as that folder is irrelevant in that case.
The wiki page [1] has detailed information on the requirements for both cold and hot backup of Alfresco.