Here is the text from Dynamics GP help file about the Effects of reconciling inventory records
There is no option to change recompilation process.
Effects of reconciling inventory records
When quantities are reconciled, the quantities recorded for the item will be reset to match purchase receipt and serial number or lot number quantities. Purchase receipts won’t be removed during the reconcile procedures. Item quantities for unposted transactions are included in the reconciliation.
The following rules also apply.
Multiple bins
If you’re using multiple bins, the quantities in the bins can be adjusted to match the quantity for the site. For example, suppose that the receipt quantity of Item A at the Warehouse is 45, the quantity at the Warehouse site is 50, and the total of the bin quantities for the item-site combination is 51. In this case, the site quantity would be adjusted to 45 and the bin quantity would be adjusted by six units.
However, the allocated quantities for bins are not reconciled to the allocated quantities for the site, but to the allocated quantities in unposted transactions. This is because items can be allocated at the site level before they are allocated at the bin level. Generally, items are allocated at the site level at the instant the allocation occurs, but items are allocated at the bin level when the fulfillment of the allocation occurs.
After you mark the option to enable multiple bins, you should reconcile inventory records. Doing so will create a bin for every item-site quantity that hasn’t already been assigned to a bin. For more information about what happens when you reconcile inventory after marking the options,
Serial and lot numbers
If serial numbers or lot numbers are missing, new serial numbers or lot numbers will be added during the reconciliation process. If you don’t want to use the numbers that have been added, you can enter decrease transactions to “back out” those changes, and then enter increase transactions for the correct numbers in the Item Transaction Entry window.
Purchase order information
Items entered on drop-ship purchase orders or drop-ship blanket purchase orders are reconciled to the Drop-Ship PO quantity in Inventory Control. The on-order quantities for items on a drop-ship purchase order or a drop–ship blanket purchase order aren’t reconciled. The remaining on-order quantity of released and change order purchase order line items and blanket line items are reconciled to the on-order quantity for the all-site of an item and each item–site combination of an item.
Blanket line items are included in the reconcile process. The control line item for blanket purchase orders and drop-ship blanket purchase orders aren’t included.
If you’re using Purchase Order Processing, reconcile purchasing information using the Reconcile Purchasing Documents window before reconciling inventory quantities. It’s important that purchasing documents are correct because purchasing information might be altered and will be used when reconciling quantities for inventoried items.
Sales order information
If you’re using Sales Order Processing, you also should reconcile that module before reconciling inventory.
