When taking a close look at the symptoms, it clearly has something to do with an overflowing save file (if you peek at their sizes, you are going to notice that they are all the same no matter what is stored therein). This means that the game’s state and your structures share the same fixed space within the save file.

First of all, there seems to be a limit to how big an individual structure can be without vanishing, and going by OP’s post there obviously seems to be a hard limit to how much can be constructed in total (not surprising, though, given the fixed size of the save files). Exceed any of those, and the structures in question are going to vanish.

Another point that crops up this way is that whenever new features are added, they require space in the save file so they inevitably reduce the space available for storing your structures.
You can see this by constructing a large enough base to hit a limit (get huge, then take it step by step: Place a few structural elements, exit, reenter and see whether or not your base still exists - backing up viable save files to cloud storage or a USB stick beforehand is highly recommended!) so that it vanishes into thin air. Then restore from backup and take a more fine-grained approach until you reach that limit.

I have had this myself in the Exiled Lands where I reached the threshold to the exact number of placeables that remained stable, but after a new feature got added, without placing any structural element, then leaving and reentering the game, POOF!!!
The entire base was gone.

This leaves one of two possibilities: Either the base design isn’t saved in its entirety any more due to the additional data introduced by the new features, or it is, but the additional data is trashing the base data, leaving it corrupted.
Then, upon attempting to restore the base(s), the routine(s) that are reassembling any bases are confronted with data that just doesn’t compute, and as a direct consequence it returns an error instead of presenting you with an invalid structure.
Given the symptoms I’d rather lean toward the corrupted base data.

2 Likes