Hello Ravi,
Removing the stock from one bin and keeping it in to same bin with movement type 999 will never double the stock. This is not possible. You are not using physical inventory procedure. If you are using source bin as 999-lost and found with movement type 712 and using destination bin as your earlier bin then it will increase the stock. Other wise there is no possibility to double the stock with movement type 999.
Please keep LS24 screen open and then perform LT01 with 999 movement with same destination bin and confirm your TO and in another screen check LS24. Compare both the screen.
Thanks,
Milind