Hello UMER
To answer your question, it really depends on what you want to do. I am assuming first of all that you are using ASA 8.X (although I believe with relative certainty that the following is supported for 9.X as well). Also, I am assuming that these tunnels are to different vendors. This is important because according to Cisco “Multiple peers used for redundancy is not supported with IKEv2 on the ASA.” Only IKEv1 supports this. So if these tunnels are redundant tunnels to the same vendor, don’t migrate to IKEv2.
Now, when you use the migration command you are correct that all IKEv1 tunnels are migrated to IKEv2. However, the current IKEv1 configurations are not removed. IKEv1 and IKEv2 both run in parallel on the same crypto map and IKEv1 acts as a backup for IKEv2.
So, assuming you issue the migrate command and you migrate everything, the IKEv2 tunnel will be created and will function as you desire (if the other end is configured correctly as well), but the tunnel you want to remain on IKEv1 will remain as such since it will fall back to IKEv1 if IKEv2 cannot be established.
You can then tweak your configuration and remove any IKEv2 configuration from that particular tunnel.
Cisco has very good and detailed documentation for this procedure and you can find it here: http://www.cisco.com/c/en/us/support/docs/security/asa-5500-x-series-next-generation-firewalls/113597-ptn-113597.html
I hope this has been helpful!
Laz