Most DTC brands keep stock numbers in at least three places: the storefront (Shopify), the warehouse/3PL (what's physically there), and the accounting/ inventory ledger (what's on the books). These three are supposed to agree. They rarely do — and the gaps quietly cost you oversells, dead-stock write-offs, and a finance close that takes days.
Pick a source of truth per dimension (physical = 3PL for units; ledger for cost), reconcile on a schedule, and rank discrepancies by severity and dollar exposure so you fix the costly ones first. Use a tolerance to suppress noise. Crucially, keep it read-only and put a human approval step on any correction that moves stock or money — automated "fixes" that write blindly cause worse problems than the drift they're chasing.
Done continuously, reconciliation stops being a monthly fire drill and becomes a background safety net.