You loaded an old save state. Search your disk for (backups) -named directories stored along with other save states and you may find one to recover you 140 hours state. If you don't know how to do this, you will have to get help from a friend. It's basic computer operation skills and we can't help you do that.

This is most likely caused by driving the GPU hard enough on your laptop for windows to think it needs to switch from integrated to discrete GPU. set your power setting to full performance and manually select the discrete GPU

it doesn't sound like you did the transplant operation correctly. you said "in a new directory", which to me means "I just made it. it's empty now" but that's not what the transplant procedure said to do.

Then one of these four things happened:
1. You accidentally deleted a file (most likely a lua script)
2. Your kid brother did it accidentally or on purpose
3. You were running everything from a zipfile instead of having dearchived it into a directory under your user control and windows lost the temp files
4. You don't understand the difference between savestates and ingame saves, and you're using savestates, and the lua script got confused, and when you load the state you restore everything to the confused state. You could solve this problem by not using savestates.

What do you expect the X button to do?
What do you expect the A button to do?
What do you expect the left button to do?

I still don't understand your question.
What were you doing with the controller in the first place?

You write "controller" and "gamepad" as if they are different things which behave differently, but they sound the same to me.
I routinely play games with a controller. Even more readily possible with keyboard and mouse to assist.
I don't understand you at all.
You may need to draw pictures with labels.

You can access whatever is contained in the previous files you find. A save state with the last in-game save should exist unless 1,2, or 3. Why do I feel like a broken record?

The information that it must be converted to sav is wrong.  Here is how to recover your data.  It is called "the .dsv transplant".
1. Clear a new directory to work in. Place the .nds and desmume.exe in there
2. Load the NDS in desmume. Start a new game. Save it. Close desmume
3. Hunt for the .dsv desmume created just now
4. Replace it with your hears old .dsv
5. Open desmume and enjoy the old save data

Search for "backup" subdirectories in the State Slots directory. Also you may be better off not using savestates at all so you can't make that error, and you should also make your own backups of documents you spend 2 months working on, or even 2 hours. Do you treat your homework so carelessly?

OK, if you say so. You offer no proof so I can only assume the kinds of mistakes people always make. And you did literally say you're using savestates. Anyway, Storm Silver is also a romhack, so it is buggy, and you will need to get help from the hackers.

It doesn't matter if anything's overwritten. There are backup files. Unless 1, 2, or 3.