Removing the set ipv6-next-hop local|global ipv6-prefix from a rule in a route-map requires the ipv6-prefix in FRR.
Trying the next fix seems to work:
--- /home/vyos/ipv6-next-hop.def 2018-08-25 22:35:35.464165100 +0200 +++ /opt/vyatta/share/vyatta-cfg/templates/policy/route-map/node.tag/rule/node.tag/set/ipv6-next-hop/global/node.def 2018-08-25 22:31:57.084165100 +0200 @@ -11,4 +11,4 @@ delete: vtysh -c "configure terminal" \ -c "route-map $VAR(../../../../@) $VAR(../../../action/@) $VAR(../../../@)" \ - -c "no set ipv6 next-hop global" + -c "no set ipv6 next-hop global $VAR(@)"