System uptime reported by Hyper-V manager appears inaccurate after Application-Aware enabled backup or replication. System uptime inside the guest OS is accurate.
The Application-Aware backup process in Hyper-V 2012 R2 will use Saved State backup if Online Backup is not available. The Saved State backup process causes the system uptime counter in Hyper-V manager to reset.
Find the issue preventing online backup, causing Veeam to use Saved State backup.
Ignore the time reported by Hyper-V Manager and instead reference the uptime reported by the guest OS.
Enable Application-Aware only for VMs which need it to minimize the issue.
After AAIP enabled backup: