After exiting my Realms world and downloading the latest backup, some region files were not filled with zeros to make their size a multiple of 4096 bytes. I noticed "holes" in the world in the map tool Minutor (probably can't handle such sizes), then redownloaded the world to make sure it wasn't just a tool issue (Realms had done another backup when shutting the world down after my logoff) and the issue was gone and the region files were now filled with zeros at the end. I did not enter the world again in between the 2 downloads. And Minutor didn't cause the issue as it only read the world.

I don't know what the difference between both backups was and why the issue happened with one and not the other. I also don't know if it can be permanent until said region is revisited inworld and what MC will do then. There has been MC-158988 where chunks got regenerated, which has been fixed luckily. Maybe I downloaded the backup too fast, before the region files were filled with zeros during the save process (all other data was exactly the same, only the trailing zeros were missing).

The issue has happened before, but only on border chunks, which I didn't take too seriously, and not in 1.14.4, only since 1.15.1 (we haven't played in 1.15). Today was the first time I explored a new area to find bees. I travelled through the nether to near the border of the explored area and ran around a little. One of the chunk "holes" was in the newly explored area, one was near the portal, and at least two in the border chunks, also nearby.

After seeing that the holes were gone in the newest download, I checked the faulty download in single-player to see whether the chunk would be regenerated (I had built something there). It was all still there, so the chunk was not regenerated. From a map comparison, it also seems as if all other chunks are still the same, so no chunks were overwritten either (as MC-158988 could have caused). So no real harm done, but still worrying how it could happen. If it's a timing issue during save, it could potentially be related to the chunk swapping issues some users are experiencing, e.g. MC-161823, or cause other problems as well.

Since I play on Realms, I can't provide any server logs. I could provide the world (before the issue, the faulty world, and the fixed one) or region files, but it's only a bunch of missing zeros, so maybe not very interesting. The faulty region file was 8.078.240 bytes, the fixed one 8.081.408 (multiple of 4096).