Sales order using one branch and a warehouse not associated to that branch.

@SunnyM Inter-Branch Account Mapping is a screen, not a feature. The feature is Inter-Branch Transactions, which is under Advanced Financials on Enable/Disable Features (CS100000). It wouldn't fix this, though. It adds Due To/Due From balancing entries between branches. It doesn't move COGS to another branch. Without the feature, a company with branches can only be set up as With Branches Not Requiring Balancing, so a mapping would have nothing to balance anyway.

In 2026 R1 the shipment creates an inventory issue, and its two sides get their branch from different places. The inventory credit takes the warehouse's branch. COGS takes the Branch on the sales order line, which defaults from the Branch on the order's Financial tab. The invoice uses that same line Branch for revenue, so COGS stays with the sale.

The fix depends on which branch should own the sale.

If it's the branch that owns the warehouse, change Branch on the order line. It's a column on the Details tab, and revenue and COGS both follow it. If you want that to happen automatically, SOLine.BranchID is the field a customization would default from the warehouse's branch.

If it's the salesperson's branch, COGS is already in the right place, next to its revenue. The transfer you're doing now is what gets the stock into that branch's warehouse before it ships.

There's also an Idea for defaulting the warehouse from the selling branch: https://community.acumatica.com/ideas/default-warehouse-by-selling-company-branch-7793