It was actually set to engrave on my normal saved settings. I did say score but meant engrave. As soon as pass through beta was selected my engrave lines completely disappeared from the screen. I wasn’t sure if that was a fluke so ran with it. Should have trusted my gut because they didn’t engrave. I may not be a super experienced user yet but do have my settings dialed in for engrave and cut on a 1/4 inch piece so I know I did that right.
So you’ve got a design file that is too big for the bed and the UI initially says “No Artwork” right?
Then you go up to the menubar and you select Passthrough (beta) does the No Artwork message disappear and the design change from gray to colored?
That’s when your engrave lines disappear?
I’ve done a bunch of engrave passthroughs with the auto-alignment about 3ft long - no real cuts though. I’ve had a couple of issues but not missing engraves.
Would you be comfortable posting the file or sending it to me in a PM?
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Sent you a PM. So I turned everything back on and here is what is happening no matter what order I do it. I start with a blank slate (nothing on the screen workspace in the design space). You are right it says No Artwork. Then I upload my design. Still No Artwork because it is too big. Then I can select beta pass through or go set my cut/engrave settings. As soon as I set the engrave settings for the inside cross marks the engrave piece disappears off the canvas into never never land. I have tried it several times and my engrave lines just disappear no mater which order I do things. 
EDIT: One thing I noticed was if I change them from Engrave back to Cut they show back up. But if I change them back to engrave they disappear again.
Could it be that your engrave settings are outside the area where engraving is possible? This can be a smaller area than cutting and i believe is influenced by the engrave speed settings. (see posts on the new engrave speeds for more on this).
I am not sure I understand. The engraving is inside the cut area and the cut part doesn’t seem to change. I will take a look at the engrave speed settings, but does this mean that settings I have used before for engrave would no longer work? Sorry for not following. I just want to try and make sure if I have “saved settings” that they don’t get rendered randomly useless if that makes sense.
With this being said I did shrink the design to well under the design space maximum size and when I selected engrave it again disappeared. So you may be right that the new engrave speed settings changed my defaults to not work anymore.
the engrave area may be smaller than the available cut area depending on your engrave settings.
look to see if your engrave is in fact, outside of the indicated area. or slow down your engrave speed (and turn down the power accordingly) to see if that helps. For example, an engrave speed of 4000 will have a much smaller allowed area vs a speed of 1000.
The inside cross piece lines are just lines - they don’t have width (to the GF) so they can’t engrave, they can only cut or score. That’s nothing to do with the Passthrough, that’s just the way the GF handles things. If you turn them into an object with fill, they work as engraves. Just make them very skinny rectangles in effect.
The diamond has both an outline stroke and a fill. You can engrave, score or cut. But since it’s the cut, the fill is superfluous.
Ok, so THANK YOU for your help! That was it the score lines did work. The cut was flawless (I will go back and update the original post. But the score line was still off a hair. But since it is going to be painted it isn’t a huge deal since the outside line was perfect. 
THANK YOU!
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I changed the cross lines to rectangles of 0.01" x the needed length and gave them a fill but no stroke. I changed the kite outline and the two holes to a stroke without a fill and then uploaded it. This is what I got with the passthrough enabled.
But since you could score, you can get the same effect that way as you saw. If you really wanted to engrave, you need to have filled shapes even if the shape is infinitesimally small like the ones in the picture (.01" wide).
You rock sir! Thank you so much for your help today!
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I signed up but never heard anything back. Is there a reason for that? Are some people not approved?
How long would it take for pictures to happen? It has been about 11-12 minutes and seems stuck on this step.
Ive never had it take longer than about 5 mins
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Two times in a row this morning. Wasted at least $12-13 in materials.
At what point is it hanging? After the first cut, or after the first time you move it?
After I cut it. Sorry for the delay. After me and my machine got in the argument earlier I had to step away. hahaha
Yes, I’ve been there!
Are you starting with your material against the left edge and the front pass-through door?
That’s how I place my material, and I’ve never had a problem.
Yes I did… twice. I am trying again after giving it a time out. I am thinking of always doing a test cut on the pass through to make sure it isn’t being moody but wish I didn’t have to. That was sa bummer to waste so much material.
Shoot. Hopefully someone else will have a better suggestion.
re material waste, I always test on a piece of cardboard that is large enough to recreate the cut I’m planning to do. Good luck!
i am not convinced the cardboard first route is of any help.
This thing is inconsistent enough for me that it literally can fail then pass on auto align ( or in the one case I tried it, pass then fail) with no changes between tries.
Also, this depends on recognizing prior cuts, and the cuts may not appear to same between cardboard and the target material.
These both suggest what works on cardboard may not work on target material , Thus, I think it may waste of time and not a means to success.