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

​@Steve Milner SO has branch BC and warehouse CA. Financial on the SO also states BC. At the shipment stage the entry post credit inventory for CA and COGS to BC. At the invoice the journal entry all hits BC which is correct. 

@SunnyM That's the expected split. The inventory credit follows the warehouse, so it lands in CA. COGS follows the Branch on the order line, which defaults from the Financial tab, so it's BC. The invoice reads that same line Branch.

If you want COGS in CA while the invoice stays in BC, there's no setting for it, because revenue and COGS both read that one line Branch. Splitting them takes a customization. The inventory issue line gets its branch in SetINTranFromShipLine (UpdateInventorySOExtension), and COGS posts to the branch on that line.

The other route keeps COGS in BC and adds Due To/Due From lines so CA and BC each balance. That's what Inter-Branch Account Mapping feeds. Between branches of one company, Acumatica only writes those lines when the company is set to With Branches Requiring Balancing. Companies (CS101500) won't change an existing company to that type once it has more than one branch and data has been posted for it.