How to flush a single SA?

I can see how to flush all SA/SPIs, but cannot see how to flush just a single SA without breaking all of the other VPN connections to the router. ie I only want to force re-establishment of Phase 2 on a single policy.

Unfortunately it is not possible, you can flush only all SAs.

If you have multiple peers, you can kill a single peer in /ip ipsec remote-peers (which will ofc flush SAs of that peer).

Its atleast a little better then flusing all SAs.