UE 5.5, Deleting a HISM During runtime causes 1 object in the hiarchy to blink in and out.

I also have the same problem, but I have solved it now.
First, BuildTreeIfOutdated (false, true) must be called in C++immediately after the number of Instances changes,this way can fix Culling Problem.
Additionally, I noticed that when the number of instances changes, other instances in the Velocity buffer will suddenly change their Velocity


so,Turn off motion blur in project settings and set motion Blur Amount to 0 in PostProcessing Volume
image
I hope it can help you