I can understand the problem - I use both Vcarve (for 2D machining) and Fusion 360 (for more complex "engineering" jobs) and they handle this kind of thing differently so you have to stop and think each time! I have just made a brass plaque - engraved, holes drilled, outside cut and chamfered - which involved 5 different tools. So 5 separate toolpaths as Vcarve can't cope with multiple tools in one gcode file unless it believes the machine has a toolchanger (as far as I can see) where F360 can mix; my machines are set up to pause for a manual tool change so that works for me.

I presume that you are using different tools for roughing and finishing? If you are using the same tool, you should be able to combine them in one file.

But you've found the trick, so it won't happen again! Probably