Okay you are using two different end mills for a project. You probe the first one when you start. Do you have to probe again when you change bits
yes you have to probe for Z when you change X and Y will stay the same
For clarity, If you use two different tools to create a project you need to create multiple tool paths. All operations with a particular bit can be saved together but if you are using different tools you must make multiple tool paths. In the design process for instance you use a #201 for pocketing and for cutting out an object. These two operations can be saved together or separately. If the project used a 302 to vcarve letters or a picture then make a separate tool path for that operation. So for instance for the 201 tool you would save the tool path as 201cutout.nc, then maybe 201pocket.nc. Then you would disable both of those tool paths and create the 302 tool path as 302picture.nc. Then enable all tool paths. So you always run the least invasive tool path first like the 302picture. You would zero for x,y and z cut the 302pic.nc tool path. The router would cut the 302 file then return to the rear of the machine. You would power off the router and jog the router to where ever you feel comfortable to change to the 201 bit. Then you would only need to set the Z zero because the X and Y are still in memory on the controller. Then you would run the 201 paths making the cutout one last. All of the tool paths have the same origin and once you set x and y they stay in memory. Just do not turn off the Shapeoko controller off. As long as the controller stays powered it remembers the x and y zero origin.
Please see: https://docs.carbide3d.com/tutorials/tool-change/ for the official documentation on this.
That information is stored in the non-volatile memory. It will persist across power cycles and only changes when you change it.
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