Lost resources from the settlement (Fallout 4)

Now I’ll tell you a story.
I got a strange bug.
I played about 60-70 hours, and got to level 49. Played for survival. Valentine has not yet been saved, the castle has not been captured, and has not really made any progress in the plot. He was engaged in collecting trash, flowers and pistols for sale, traded in trash.
Huge quantities of components have been accumulated, thousands of copper, hundreds of nuclear material and tens of thousands of steel and wood. Well, you get the idea.
But one terrible day I decided to try building a dog cage. As a result, of all the components, only a little wood and a hundred copper remained. Those. almost all the resources that were there are gone from the workbench.
Nobody plundered the settlement. It turned out that a dog caught in a cage was considered a game as an attacker.
In general, I do not know what the matter is, but as soon as I build a cage, after a few hours of the game, almost all the components from the workbench disappeared.
But since I played on survival then there were only 3 saves. Well, in general, I noticed it late, and I didn't have a save until the cage was built.
Here is such a setup from absent. I think it makes no sense to continue the game, tk. I cannot correct absolutely nothing.
Almost a month of playing in the evenings. Now start everything from the beginning, swing from level 1 again.
I'm shocked. There is no desire to play again. The game was released many years ago, I play from the start, but it has not passed. Probably started over 15 times already. And then again everything was gone.

There would be not 3 saves, but more - I would have lost at most a day of the game, but not a month. Thank you for being so stupid.

Question. How to hide something so that no one can pick it up?
If the settlement is looted, will only the contents of the workshop be lost? The contents of the boxes have not been touched, are they? It seems like everything remains intact in the boxes.
If you hide weapons and ammo in the workshop, will they all disappear too?
Is it true that settlers can take weapons and ammo from the workshop? I heard that they can.
In any case, I understand that it is better not to store anything in the workshop, except for weapon mods.
But can you be sure about the contents of the crates built? It seems that when attacking a settlement, boxes are not looted. Or can they also plunder?

Boxes (man-made of course) are generally available in my opinion even to settlers and other NPCs. I saw more than once how during an attack on a settlement some Struggers, or maybe even a simple settler, ran up to the box and stole weapons from there. At the same time, they steal strangely, if there are 200 carbines, then he will take all 200 carbines. Cartridges and other weapons are stolen in the same way, and in the same way everyone at once. There were 400 grenades and 60,000 cartridges for plasma lying there - and so, apparently, he will take everything at once. But what if some kind of settler know-how climbs in and steals some kind of Last Judgment or the Righteous Sovereign and the entire supply of nuclear blocks and batteries? And then it disappears somewhere or dies.
In my opinion, it's not okay that some kind of settler can climb in and take all your cartridges, or some legendary.

How to resist this at all? I do not understand. I even saw Karla-Urna climb into my box and steal shock rods from there. What if it were a shish kebab? How can you then take it away from her? What is that all about?
Well this is nonsense. You never know if everything is intact.
I tried to put a ladder in the sky and there is a box at the top. But what will prevent them from climbing the stairs? I climb like that, so they can. First, every time I dismantled the stairs so that they could not climb. But it is stupid to rearrange this ladder every time. Then he made sills in the air. Just squares of a tree at different heights. I can jump on them. And the settlers don't seem to.
But here, too, there is no confidence to be honest. For settlers often spawn on rooftops. I have no idea how they ended up there physically, they could not get there in any way. And they also have some kind of fence radius. Once I put the boxes in the air on wooden floors, at a height of about a couple of floors. And then I saw how a thief running under this structure was picking up something from the ground. It turned out that he had robbed a box that hung from 5 meters above his head and, moreover, not only hung, but stood on the floor. And he somehow through the floor and through all these meters of distance was still able to steal everything from there. For the same reason, it is useless to build deaf houses. For the settlers are thieves and can steal through a five-meter concrete wall.

In general, there is a problem and I do not know how to solve it. I really do not want to then, after a hundred hours of play, discover that again something is missing and the legendaries. Maybe there is some kind of mod for an unattainable box? That no one could stick their sticky paws in there? Tell me pliz.