Do you see any events on the firewall side for the periods, when it happens? The encryption level itself should not have affected the way the jobs operate, I suspect there may be tcp timeouts for IPsec tunnels or a potential resources saturation on the endpoint firewalls, which may lead to the packets drop.
Product Architect @ SingleHop - Veeam Platinum Service Provider
VCAP-DCD, VCAP-DCA, VCP-NV
Veeam Certified Architect