How are you creating your toolpaths ? The "sequencing" for toolpaths generally comes from the program you are using for CAM. Flashcut, as well as any other CNC control simply just runs the code created by your cam program, in the order it was saved or exported.
However, If by chance you are using the DXF import part of Flashcut to create toolpaths (g-code), the only good way to sequence the order of your cuts are going to either be to find out how to reassign the order of entities in your cad program before exporting them as DXF (some programs allow this, some do not), or, export select entities in job groups, such that you can run a "job" of just the inside work, and a different job to cut the outside work based on that of your scenario.


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