I tried some world recovery with mcedit, and one of the mods are leaving behind empty entries. It seems that it might be yours, i'm still unsure, but i would suggest investigating.

The scope of this mod is within Minecraft. Anything MCEdit is doing is a problem on MCEdit's end.

Well,something in that world also caused issues with remain in motion (thinking it through, i might check that side as well) as well, and carpenter's blocks are one of the things whitch are got broken (i have a few other suspicious mods).
Right now, i will just save what i can save into a chest and import that.

And its turned out to be entries without x coordinate. There were empties as well, but i can't see anything else.

Empty or not, if MCEdit is causing issues outside the game it's not a concern on my end.