Very interesting observation. I used HxD to see the headers and they are indeed sometimes gone. Plus saving IENERGY increased the size. I think it will be wise for me to save everything again and commit those changes. This might actually help Lucius when he starts again working on voxel support for TFE (I vaguely remember he did mention something about headers on Discord server...).
EDIT. Alright, I updated all voxels (expect custom mouse droid, that one I have to redo anyway), all headers should be correct now.