After server transfer, incremental backups don't have hard links to full backup

I transferred sites off a CentOS 6 server to a CentOS 7 server. Both servers are using incremental backups. Both of them support hard links in the backup storage. On the old server, if I go to a backup directory for a site and look in the public_html folder, all the files show up. If I do the same thing on the new server, only changed files show up. It looks as though the backup process on the new server never created a full backup of the site to base the incremental backups on. How can I force the incremental backup process to make sure there's a full backup to work off?