Thank you, but none of the suggestions worked. Here are the steps I followed to reproduce the issue. I explain my setup and then the steps I followed based on your suggestions to achieve my goal.

First my setup:

1. I created 3 part items, named "Mix", "Milk", "Eggs". Each of these items are assigned to a "Sales" income account and an "Inventory Asset" asset account.

2. I created 1 assembly item named "Pancakes". This item is assigned to a "Sales" income account and an "Inventory Asset" asset account. It also includes all 3 part items above.

3. I entered a "Bill" transaction type to purchase the part items (Mix, Milk, Eggs) and have an initial inventory stock.

4. I built an assembly for the assembly item, for only 1 batch of pancakes which includes the 3 part items above.

Before I get to my change, first an explanation of my goal... At this point all transactions are using the "Inventory Asset" account. My goal is to change the transactions to put my part items (raw materials) to a "Raw Goods Inventory" account and my assembly item (finished product) to a "Finished Goods Inventory" account.

Now my change:

1. I changed the income account for my 3 part items to "Sales of Raw Goods" and the asset account to "Raw Goods Inventory".

2. I changed the income account for my 1 assembly item to "Sales of Finished Goods" and the asset account to "Finished Goods Inventory".

3. I verified the data.

4. I rebuilt the data.

After this, the only transactions who's accounts changed were for the "Bill" transaction type. Instead of having "Inventory Asset" as the account, it now has "Raw Goods Inventory". However, the accounts for the transactions related to the "Build Assembly" transaction type did not change. They still say "Inventory Asset".

I've attached an image that shows the results.