It is really strange, at first I thought it is a purely KRO bug.

But finally I have conducted one test - acquired SR-71 (AS-3), launched a missile, when the target started jamming I switched on POMECHA switch and re-acquired the target (AS-4) and waited.
The only launched missile (with POISK V VKL and AS-3) in the moment of reacquistion of the target switched off KRO transmitter and GSN reacquired the target! After some time the target was destroyed with this missile. No other missile was launched.

So this behavior is strongly unprobable. How the missile could know that GSN of missile in flight has to switch to home on jam mode?

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EDIT
After SR-71 started jamming I have not touched anything except POMECHA switch, AS-4 switch (fi indicator is lit) and AS-RPC.
NO PROLONG, NO GSN mode change or anything else. Everything remained in the same positions as in the moment of launch.