You have to create the BOM all over again. Else the nesting will not come out okay.
While building BOMs you need to consider how the BOM will get used. Let’s say you have a Nesting like this:
ProductA > AssemblyP > RawMaterialX
Now the Exploded BOM for both AssemblyP and ProductA is RawMaterialX if you build the BOM for AssemblyP first and call the AssemblyP BOM when building ProductA BOM. If you are not careful and if the Is Default is checked, the BOM will get automatically pulled when using an input item that has a BOM into the BOM for another item.
Now let’s say you make the entries just once after ItemA is made. Then all you need to do is flush out RawMaterialX. Because you never made AssemblyP, there is no need to flush it out.
But let’s say you make the manufacturing entries for AssemblyP which has flushed out RawMaterialX. Now you see AssemblyP in your Stock Balance report. Now, while making ItemA, you (rather the user making the manufacturing entry) should take care to ensure that Use Multi-Level BOM is unchecked. Else you run the risk of flushing out RawMaterialX twice, especially if you’ve called AssemblyP’s BOM in ItemA.
Since users cannot be expected to remember these details, I like to, for my clients implementations, build two BOMs; One for Raw Material Planning. And the other for passing Manufacturing entries.
The BOM for Raw Material Planning is a nested BOM, so that users can know the quantity of RawMaterialX that is necessary to make X quantity of ItemA. While the BOM for Manufacturing is built to ensure that only the Items that need to flushed out is in the Exploded BOM of the Item. This is just so that there is no chance of user errors.
So, managing BOMs on ERPNext is indeed complex and we need to make it simpler, yet have adequate controls for users.
Not sure if this helps, but that’s the complexity you have to deal with.