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If you did it that way round and the groove was quite close to the window, you will have only a very thin strip left to work with which may be tricky to cut.
If I did it that way I would want to tape the fallout back in. When you cut the edge off the vgroove there will be no support at yhe middle of the mat drop out so I would think you risk the vgroove not being consistent unless you tape it all together. If its taped together then wjen you untape it I think you would risk damaging the backside of the mat...
But to answer the question you can cut the vgroove in either order I just think that it would be easier to cut the vgroove first.
The only problem I can see with cutting the v-groove after cutting the opening would be if you use a c.m.c. Like the Wizard. If you cut the opening from the back then turned the matt over to cut the v-grove and your card wasn't exactly, perfectly sized or was a smidgen out of square the v-groove would not line up perfectly with the window.
The Wizard cuts v-grooves first by default and when v-grooves are specified it cuts openings from the front. Changing the order probably wouldn't cause a problem unless it is a narrow mat and not set as "cut the outside".
I would personally always want to do it first, but we learn by trial and error and you may find that it works better for you to do it the other way around!
I am going to reiterate my main concern and that is with a long leading edge, and a thin "supporting edge" behind it, when you go to shave off the 1/16th inch lip the shearing pressure from the blade may push the edge inward and you'll get an inconsistent cut, I fear really thin in the center.
Anyone else agree or think I am crazy in my concern?
I have done vgrooves "backwards" before, like you a re considering, but I did tape the drop out back in place, to provide strength to the v-groove lip for cutting. That may have been overkill on my part, call me a chicken but I didn't want to find out on a paying customer's artwork.