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With FlashCut CNC Version 4.0, you simply change the system units under the Confguration…System…General menu.

For older versions a setup file with English units (in) can be converted to metric units (mm) using the methodology described below:

Open the Setup File that currently runs your machine properly by going to File > Open Setup on the FlashCut CNC Main Screen. This file may already be open if you have been running your machine recently.
Go to the Configuration > System > General Configuration Panel and switch the System Units from English (inch) to Metric (mm). This will change the units throughout the FlashCut CNC software from inches to millimeters, but will not convert values.
Using the tree on the left side of the Configuration Dialog Box, go to the Mechanics Configuration Panel. Divide each of the Screw Threads by 25.4. Multiply the Axis Lengths and Backlash by 25.4.
Using the tree on the left side of the Configuration Dialog Box, navigate through each individual setting in the Configuration Panels and multiply each value with (mm) or (mm/min) as the unit by 24.5.
Go to File > Save Setup As on the FlashCut CNC Main Screen in order to save your new configurations settings in a different Setup File. You may want to give this new Setup File a distinctive name like “METRIC Version.STP,” or something along those lines so that you do not confuse your new metric configuration with your original one.
You can now easily switch between inches as millimeters as your units by opening the setup file that corresponds to the units that you would like to use.