Aditya,
Thanks for your kind words on the Analytics module :)
We are shortly going to release the Accounts-Inventory integration (Nabin will post more on this). With this, Stock in Hand will be automatically updated from Purchase Receipts and Expenses from Sales Invoices. So having the right valuation will become even more critical.
In your case where your current valuations are all messed up (and I am sure there are other users too, because the system does not give incentive to update correct valuation via Stock Reconciliation), what you should do is.
1. Make a Journal Entry to update your correct Stock in Hand based on your actual stock.
2. For entries post the date we release the integration the Stock-in-Hand + Cost of Goods Sold will be automatically updated.
3. For earlier entries, you will have to manually check the ledger postings at the time of Purchase Invoice and Sales Invoice till all the older entries are out of the system. The system will allow you to manually edit the ledger postings in case you need to make an adjustment.
This will all happen post we release our Accounts-Inventory integration module, which we are testing at the moment. Hope to release it soon.
best,