I rolled back to a time when I didn't move those things, and kept going from there with new ideas in mind.
It was less me being upsetti-spaghetti over not having containers to work with, and more disappointed that I can't show the natural evolution of the landscape due to human interaction. I mean, it's a big ol' barge filled with washed up stock, and now my settlers are just gonna have to ignore that it's there? Oyy... talk about ludonarrative dissonance. Oh well, the fight goes on.
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Having watched that video you linked and done a bit more reading, I've come to a possible new issue. Literally anything scrapped via Place Everywhere's extended scrap options will cause issues with precombines, won't it? The piles of debris in the wrecked house, errant rocks, boards and planks affixed in areas they're not wanted?
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Also (possibly a lesser problem, but one I wanted to bring up regardless), pre-placed items that can be moved and scrapped sans mods disappear and then fade back into reality when moved; as an example, in the garage near the wrecked mansion I picked up and moved the diagnostic cart it disappeared (but the green highlight of the object remained) until I placed it back down, whereupon it sort of fizzled back into existence.
Is this normal? I've never seen this happen before.