The way you describe the staging works is very inadvisable for two reasons.
1. Your site is more than just files; it's also database contents. Since the staging does nothing to copy the database you essentially have two sites which read from and write to the same database. This is not a staging site, it's a disaster in progress...
2. Putting the staging site in a subdirectory of the main site means that the .htaccess of the main site is applied to the staging site and this causes all sorts of issues as warned in https://www.akeeba.com/documentation/akeeba-backup-documentation/restoring-backups.html#general-guidelines (see “Do not restore in a subdirectory of your main site” and “If you are restoring on a subdomain, make sure that the subdomain's root directory is NOT a subdirectory of your main site”).
So my advice would be to not use this problematic workflow. You can always take a backup of your site with Akeeba Backup — the free of charge Core version is enough! — copy the archive to the subdomain's web root folder using the hosting control panel's file manager, upload kickstart.php there and restore the site using a different database to the one used by your live site. Transferring from staging to live is the opposite process: backup the staging site, restore to the live subdomain.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!
