The game's worked smoothly....so far. I'm at the mission where the Sole Survivor has to find Nick Valentine. Stocking ammo and caps is getting pretty hard now, so I decided to focus more on my settlements. However, whenever I deposit anything in the Workshop at any settlement, and then try withdraw it/them, there's nothing there. And I've lost a massive amount of resources because of this.

I tried reinstalling the game, updating it regularly, etc, but nothing actually worked.

Can someone please help??

It's possible you have not lost anything, you just do not understand how the workbenches actually work. If you deposit a gun or piece of armor at Sanctuary, you cannot retrieve those items from the workbench at Red Rocket Station (but if you go back to Sanctuary, they are still available to be withdrawn). Workbenches are not universal storage vaults.

You can share building and crafting resources between settlements that have a supply line set up between them (setting up supply lines requires the Local Leader 2 perk).

To elaborate on what BrotherGrimm explained, food, water, and crafting resources of all types are shared between settlements connected by supply lines. However, this is only on an "as needed" basis. It does not mean that inventories are shared for these items, only that any settlement in need due to food or water shortage, or you attempting to craft something there when there is a shortage of needed components, will acquire the needed resources automatically via the supply line (and only the resources needed, nothing extra). You can't see shared resources in any inventory, not as separate elements/items. You only see total available components for crafting which are all components from current settlement + all components from supply line connected settlements.