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My SO is quite lazy about putting things back "where they belong". Not surprisingly, she is very good at losing things and not being able to find them. While I will often help her find something she has lost and gently remind her where I looked first, in general, when you have a problem, it is best to jump straight to the solution, rather than to analyze the cause. This works for both interpersonal and professional problems.
"Is it ok if I send you a text when you're late? I worry about you and just want to make sure you're ok. I get paranoid and might send out a search party! ;)"
"How can I help you remember where we store the important documents? Shall we go through some unfiled papers and practice together?" For "proper place" type problems, it is actually helpful if your SO also regularly loses things. "Can you help me find my coat?" "Sure, where did you look first?" "Uh, in the bedroom, I guess." "Well, I'm going to check the coat closet, because that's where I put it when I find it laying around." After about 10x of having this exchange, they become more biased towards putting things where they belong. Also, they are more likely to anticipate your first response, because it's predictable, and this shortcut also helps motivate the desired behavior. Let's be honest: the answer to: "Why didn't you put this back where it belongs?" is: "I was lazy and I didn't care." So forcing someone to give that answer doesn't get you closer to the desired solution.
Practice Makes Perfect
Another strategy for this kind of thing is to say: "Well, we have a bit of a mess here, don't we? Can we spend 30 minutes tidying up?" Before you start, note which things are out of place so you can look for them when you're done. When you're done, try to find all the misplaced items in their "proper" location. If something is out of place, you can say something like: "Hmm...I expected to see your coat here in the closet, but I don't see it. Did you happen to see it while we were cleaning?" "Oh, I uh, hung that on the back of a chair I guess." "I see. Is that where you planned to look for it the next time you need it? Because if I help you look for it, the first place I'm going to look is here in the coat closet. Finding it there will save you some time when you're late for a meeting."
So don't approach it as a scolding or punishment; but rather, the future reward of doing things in a more disciplined way.
Also, if my SO is really late for something, I just send a text like: "Hey, I hope your event is going really well! Haven't heard from you in a while and just wanted to make sure everything is ok." So the point is to remind her that I fundamentally trust her, but I am concerned about her well-being and will step up to help out if she really did encounter a problem (like locking the keys in her car, getting lost/stuck/etc.).