1.11.2 Forge 13.20.0.2300 RecurrentComplex-1.4

Region was deleted and reloaded.

It did not, I tried deleting the region twice. Same issue.

However, I started a new world with the same seed and the structure is there, without the space blocks.

Not sure if it should have it's own issue but i had a similar problem.
my saved crashed because of the recursive mod chunk loading and when reloading the save i had this (see screenshot below)
Version: RecurrentComplex-1.4.1.jar
with other crashes i have not being able to recreate the appearance of those blocks

I probably should have mentioned that the reason I deleted the region was that I had the region rendering crash and was unable to get the save to load. It was a new world, so deleting and restarting was not a problem.

New world, no regions deleted, but there was a chunk rendering crash (reported in another thread on this site). This is just ugly:

I was not able to reproduce this yet by deleting region files. It seems to me the structure sight saves improperly without saving its transformers. Can you send me the reccomplex-structuredata.dat file for one of these saves (and the coordinates for the affected structure)?

I think I tracked the problem down. Let me know if this happens in 1.4.3.1 forward.

This appears to be the same problem i was having which I had to resolve by deleting the DAT files as well as the region files.

Hope it's fixed in the new version.