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How to add existing stock to the system?

I’m trying to add existing stock to my database. I tried using stock entry to do this but the system has negative total value difference. How am I supposed to do this properly?

That is correct. That is because you have a value for Total Out (Target Warehouse), but you have no value for Total In (Source Warehouse). That is why 0 (in) - Stock Value (out = - Stock Value (negative Total value Difference).

You may enter a journal entry for this Stock DIfference (check the chart of accounts ledger where the value of the stock difference is posted) to post this stock difference value to its proper gL account

Should I be doing it this way or should I be using stock reconciliation?

If you want to just add stock to a warehouse for any item, you can directly create a stock entry of type= Material Receipt. Only mention the Target Warehouse as shown below.

This will add stock for that item in the target warehouse without disturbing the stock value in the other warehouses.

Either way is good. But I remember that Stock Entry Material Receipt is better. (When you click the Title part, you can change the Title to Stock Inventory or something like that.)

yes. you are right Stock Reconciliation is the correct way.

You can see the pros and cons of two approaches in this thread.