This is a crazy idea but... Did you by any chance run that´mv logs /home/user/MyDocs´ with the phone connected to the PC in the USB Mass Storage mode? If so, try the Mass Storage mode again and see if the folder magically reappears. You will need to check it on the phone though, not on the PC.

Regarding your other two questions. Yes, you can delete '._'. It is something to do with Mac, IIRC. If you do not use a Mac, you do not need it. To be honest, I am not sure if you need it even if you do have a Mac. All I know is that I deleted it years ago, along with other Mac related files (sorry, for the life of me I can't recall their names now) and never missed them.

The Trash-1000 folder is a Linux equivalent of the Windows Recycle Bin (more correctly, not Windows but Windows Explorer and not Linux but Nautilus, but we do not need to split hairs). In other words, it is a temporary repository of your deleted files. Have a look what's inside and if nothing important, feel free to delete it.