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Just to be clear:
Changing acceleration values during Gcode execution IS possible. But the changed values are only used AFTER the interpreter has encountered a queuebuster command (eg M66 E0 L0) in the gcode which forces a synchronization between the interpreter and actual motion control.
For an example of how to use custom MCodes to change ini values (eg axes-limits, -velocity and -acceleration ) see the included 'millturn' simulation config where these values are changed using M128/M129:
github.com/LinuxCNC/linuxcnc/blob/master...millturn/mcodes/M129

The queuebuster command (ie M66 E0 L0) is located in the preceding 'M428/M429' remap that call 'M128/M129' respectively:
github.com/LinuxCNC/linuxcnc/blob/master...ap_subs/429remap.ngc

The split in MCodes is necessary because it is not possible to set halpins directly through gcode but only through a hal command. On the other hand it is not possible to issue gcode commands to synch the interpreter using a hal command.

So what all this means is that changes to axis acceleration have to be inserted into the gcode program prior to program execution.

Hello Todd,

Feed Override does work actually, but the accelerated max speed for the 3D and 2D movements are become different. For reference i have attached one image where 2 different section is marked with numbers, mark 1 section has Z movement and mark 2 do not has Z movement this makes section 2D movement.

Now, when tool slide down from the leaf of flower if feed override set to 10% then speed reduce to some speed x but when running in between leafs the machine speed reach to 3-5x due to x-y acceleration. really required is feed percentage should set all the axis speed to same level and maintain that speed between part1 and 2.