When first discovered, I rejoined my SPG after some days, and found chunks missing from the original, but didn't want to try to debug so I attempted an admin load to just get a clean copy, but that came up with identical missing chunks. So I assumed I'd made some catastrophic symmetry error before saving and exiting my last session, went ahead and rebuilt the ship (patched the missing chunks), thoroughly looked over my ship for quality in build mode and 3rd-person and it was perfect. So I quit and immediately rejoined to make sure it was still good but it wasn't. I found similar (unsure if identical) missing chunks on my rebuild and admin loads all had copies of the error, so this time I knew it was not my mistake and started trying to pin it down.

I next assumed that the core was corrupt (I've encountered a kind of issue with simple drone miners not working in the past - I did extensive R&D with them at one point - that was often cured (across worlds) by spawning a brand new core and building the drone again from scratch. The new copy would often work indefinitely, despite being an exact copy of a drone that had previously worked fine, then stopped working completely and permanently (across worlds)). So I tried it again with a new core and everything was fine for a while, but I may not even have logged out (unsure) but went on to do some weapon tests on the shell, deleted it, and the admin load had the error.

To eliminate the possibility of the world being corrupt as well I created a new world, spawned in, and started rebuilding. I wanted to get an idea of if a specific system might be causing the issue, so I started out to save it at every stage and re-join. It ended up happening with my first save-check, and all I'd added was the fill-in of the build-helper ellipsoid. In this case - new world, very first thing spawned - I definitely quit to desktop, re-joined, and immediately the ellipse I'd filled had these missing chunks. All admin loads also had them. It didn't make sense, because I had been using build-helper ellipsoids a lot recently with no problem.

I tried again immediately with a new core. Just tried it real fast using my core as the point to which I set the build-helper. Filled the ellipsoid and save, quit to desktop and rejoined. No problem! Admin loads were clean. Quit to desktop again and restarted computer - the original of this one was still fine and admin loads were fine.

Then I tried it again using an offset point to center the ellipsoid. On quit to desktop and rejoin this new original iteration had those similar missing chunks and all admin loads were similarly corrupt.

So it's not a one-off random entity core corruption, it's not a corrupt world, it's not the build-helper because the exact same hull stays good when it isn't off-centered from the core... It has been very predictably reproducible for me with this specific shape and core offset. I have yet to test other large shapes or offsets, but will advise if I do.

My best guess is that it's something to do with the way entities now re-center their HUD icon (or some branch of the object that GUI function is calling to determine where the icon should go) based on mass. Something in that region seems to be at fault, anyway, but I haven't studied the details of other similar incidents from other players, I've only heard that they happen sometimes, so I don't have full context.

Ok... this is way more extensive than I suspected. I ran some more tests with just straight grey standard on fresh cores and the results are not good.

Testing cubes and sheets, pretty much every large shape (at least one dimension over 100m) immediately comes back with missing chunks if saved and admin loaded.

Loaded a 150m light frigate from a month ago and resaved it under a new name - no problem, no missing chunks, but recreating a roughly similar shape from scratch results in missing chunks on admin load, even if smaller.

Worse (or maybe better) I used symmetry to place 4 identical 50x50x50 cubes of grey basic on nothing but a core. Tested it and the admin reload came back with bad chunks. Worse though, without leaving the original core I hit UNDO, removing the 4 big cubes, and attempted to move. Ship's general stats says it has one block, but it moves around wildly, has 660K shields, and 132K reactor HP in the GUI although the ship stats in build mode say no power, no shields, 1 block. When I turn, the core flies about wildly at extremely high speed as if it was on the end of a very, very long stick (like hundreds of meters - possibly thousands). I feel like that actually confirms my earlier suspicion about it being a problem with something relating to the way the game's engine tags the center of mass on an entity, which is why I say it might be better since it seems to point to a similar area of code for the problem.

In the new release version (201.129 - didn't test it in the initial weapons release version) I am not able to reproduce this problem at all. It's gone and I can't recreate it. It went from every large shape being instantly corrupted, to no problems at all, so... will advise if I catch back up to it.

I came across this bug in a much different way, I imagine it could be related. However I could not replicate this again.
I created a drone miner, and set it to mine near an asteroid until I could upgrade it. I upgraded it after removing every block except the core. I rebuilt it using more blocks. I left the sector and asked the fleet into formation. As my drone reached the flagship the outer edge was the new ship, and the center was the old ship. Both were merged together.