Sometimes there were some issues with IPSec VPN tunnels on fortigate. Here some commands to clear the SA Sessions.
List the Tunnel VPN:
diagnose vpn tunnel list | grep name
Choose the name that you want to reset
diag vpn tunnel flush *Tunnel_NAME* diag vpn tunnel reset *Tunnel_NAME*
If this not works clear the sessions on firewall:
Create a filter which the IP that you want to clear.
diagnose sys session filter dst *IP_THAT_IS_STUCK*
Show if the filter shows the correct lines:
diagnose sys session filter
If is everything ok, clear the session:
diagnose sys session clear
Then flush and reset the VPN again (In both sides)