Well, I usually use that command to terminate a tunnel, so I think is not strange. In theory, the ISAKMP channel is used for authentication a key regeneration (as far as I know), but if you end it, you end the IPSEC tunnel too.
I think you may be getting ike, isakmp, and ipsec confused. Ike is another way of saying isakmp. Ipsec runs on top of ike (isakmp) so it stands to reason if you clear out ike(isakmp), then your ipsec sa will vanish too.
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We have configured the outside and inside Interface with official ipv6 adresses, set a default route on outside Interface to our router, we also have definied a rule , which also gets hits, to permit tcp from inside Interface to any6.
In Syslog I also se...