Acabei de verificar um dos meus. Você tem estas opções:
R1#clear crypto ?
call Clear crypto call admission info
ipsec IPSec
isakmp Flush the ISAKMP database
mtree Clear Mtree Manager Command Stats
sa Clear all crypto SAs
session clear crypto sessions (tunnels)
R1#clear crypto isa
R1#clear crypto isakmp ?
<0-32766> connection id of SA
<cr>
R1#clear crypto sa ?
counters Reset the SA counters
map Clear all SAs for a given crypto map
peer Clear all SAs for a given crypto peer
spi Clear SA by SPI
vrf VRF (Routing/Forwarding) instance
<cr>
R1#clear crypto sa peer
R1#clear crypto sa peer ?
A.B.C.D Crypto peer name/address
vrf VRF (Routing/Forwarding) instance
R1#clear crypto sa peer
clear crypto sa peer fará o truque