I just experienced a very frustrating snag. My last print of key tags on mirror acrylic just crashed with the following error: “AIR ASSIST FAN. Air assist fan on printer head is not running at the correct speed. Try reseating your printer head follwoing these steps, and remove any magnets from the print bed.” Now, I have used magnets many times and never had an issue, but this time the print head came close to one of the magnets and, I assume, the magnetic field interfered with the fan… which, of course, is an electo-magnetic device. After all was said and done, I lost the print and wasted half a sheet of mirrored acrylic, but the lesson was learnt. If you use magnets, make sure the print head cannot come within 3-5" of them, or you to will experience the frustration of loosing a print, right in the middle… Take it from me, it is not fun.
It’s a known thing. Personally I’ve never had the issue. I use rather large bar neodymium magnets too. But some people do have the problem. Time to switch to pins. 
You can also use magnets with shields (pieces of metal on the top side).
The thing is - you don’t need to lose your sheet if something happens mid-print. If you do not move anything in the material or the design then closing the lid and hitting print will re-run in exactly the same place, every time. If you don’t want to re-cut the area you’ve already done you can either cover the part already done with tinfoil or other non-cuttable material - or edit your art to remove the part that was already done.
No need to waste material!
Your advise is appreciated, but, in my opinion, the material was wasted as 2/3rd had been etched and to rerun the etch would make the depth unacceptably deep. It is my normal practice to etch before cutting, and due to the complex etching, it was not an option to rerun that portion. Unfortunately, Glowforge will not allow you have access to the code going to the machine, therefore, you cannot, selectively edit, and remove already run code, like you can with a 3d printer or a CNC machine.
My comment was not to argue against magnets, but to point out the risk of using them if you are not aware of their placement, in relation to the print head movement.
Before the air assist speed sensor was enabled I used to use very strong magnets every time. I could watch from the rear and see the air assist fan slow or even stop as the it passed over a magnet.
Totally your choice - but if you read what I wrote you’d understand you can either rerun protecting the part that was already done - or - edit your art in the program you created it in. Refusing to do either is choosing to waste material, and you seemed upset by that choice so I wanted to make sure you understood your options.
@deirdrebeth suggestion of editing in the design file should work. Use the coordinates in the app to make sure you place the remaining at the correct spot. I have had to recover a few designs before and most my designs are complex floral based.
This is the part that I would just like to add a comment on. A large factor is also the type of magnets used in the machine as well. Recommending simply that magnets do not come within 3-5" of the print head might be a little misleading but I respect that it is your recommendation to make. I use ceramic magnets (which have a much lower BHmax then neodymium magnets) but I know others use neodymium as well with proper mitigations to prevent the fan issue. It is important to always make sure and research into anything that is put in the machine and not generalize materials.
I used a lot of magnets before they added that sensor, and I now realize that they were messing up my cuts while I thought it was the fan loading crud. There are “capped magnets” that keep most of the field going down and I have also discovered that an array of tiny magnets can have a strong but very limited fields,
It is very easy to wave a screwdriver or needle file above the magnets at the height of the head, and if you can feel the magnetic field so can the fan,
This question is outside our team’s scope. I’ve moved it to the Beyond the Manual so the discussion can continue there.