How do you stop embedded magnets from shifting when the print resumes?

The trick that fixed this for me was pausing a couple layers above the pocket instead of right at the top of it. So the magnet drops in, sits on a solid floor with a little bit of filament alredy printed around its sides, and then there's one or two more layers of wall going up before the roof closes over it. That way the nozzle never comes down right on top of a loose magnet, it's bridging over a shallow recess instead. I set the pause for the layer where the roof of the pocket starts, not the layer where the magnet is flush. On the 5M you can set the pause height in the slicer and it'll park the head off to the side, which helps too.

Also make the pocket a hair deeper than the magnet thickness, like half a layer or a full layer worth. If the magnet sits even slightly proud, the nozzle catches it. If it sits slightly recessed, the roof bridges clean over the top and you never feel it. For the glue, super glue works but a tiny dot in the center of the pocket floor, then press the magnet down with something plastic and hold it a few seconds before resuming. If it still tilts, your pocket might be a touch too wide, so the magnet can rock. A dab of hot glue in the bottom actually helps there because it fills the gap and grips the sides.

Polarity tip that saved me a bunch of redos: before the print, stick all four magnets onto one bigger magnet or a magnetic tool holder with the same face out. Then that face goes down in every pocket and they all match. I used to sharpie the north face of each one, but the stack trick is faster and you can't mix them up mid print. PETG should be fine with all this, it bridges okay. I'd just do a test piece with one pocket first before committing the whole cowl again.

Reminds me of the days we'd just glue magnets in after the print was done. Design the pocket with a solid floor and no lid, drop the magnets in once it's off the bed, cap it with a dab of glue and a little printed disc or just leave it recessed and fill with epoxy. Zero risk of the nozzle hitting anything, and you can fix a flipped magnet with a knife tip instead of trashing the whole plate. Slower, sure, but back then we didn't have pause-at-layer anyway, so old habits stick. Does the cowl let you get away with an open pocket on the inside face? The display stand would never see it.

I do the same thing with magnet pockets on smaller jobs and the one extra thing that saved me headaches was dropping a single drop of CA glue into the pocket, then hitting it with a puff of accelerator spray before I drop the magnet in. Sets up in about two seconds so there's basially no chance of it sliding when the nozzle comes back around. I've been running a print farm for about three years now and prolly done 40 or 50 of these pause-insert prints, that combo plus a slightly oversized pocket has been bulletproof so far. Worth a shot on your test piece before you commit the whole cowl again.

New here so hopefully this is ok to jump in. I never got brave enough to pause mid print, I did something similar on a cabinet latch cover where the magnet sat under one top layer. You can see a faint ghost of it thru the surface which bugged me til I sanded lightly and it mostly disappeared. Do you find the bridge over the pocket leaves a little dimple on the cowl, or does PETG hide it pretty well once it cools?

Update: tried the pause a couple layers above the pocket like the first reply suggested. Dropped the magnets in on a solid floor with walls already around them, then let the roof close over it. Both seats came out clean and they actualy grab the stand now instead of pushing off. Wish I'd asked sooner.