I have done a similar case and during the investigation, I found that the value of rec_net_weight_ variable (net weight of the part) is having a value even though the value of net weight of part is null. The variable: rec_net_weight_ is defined in the Shipment_API.Get_Net_And_Adjusted_Weight___ method and when the value of net weight of a part is null, the value of rec_net_weight_ variable will be previous value inside the for loop. This bug has been fixed by UPD13 patch 159682. Most probably it will fix your issue.
As a workaround you can set Net Weight to 0 in Part window → General tab.
I have done a similar case and during the investigation, I found that the value of rec_net_weight_ variable (net weight of the part) is having a value even though the value of net weight of part is null. The variable: rec_net_weight_ is defined in the Shipment_API.Get_Net_And_Adjusted_Weight___ method and when the value of net weight of a part is null, the value of rec_net_weight_ variable will be previous value inside the for loop. This bug has been fixed by UPD13 patch 159682. Most probably it will fix your issue.
As a workaround you can set Net Weight to 0 in Part window → General tab.
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