Hi Dheemahi,
Please make sure that an entry with KEY is also maintained. Also, i have found some SAP notes for BOM deletion transfer. Check if anyone of them is applicable in your case.
SAP Note 1563191, 1711850.
There are many more SAP notes on BOM transfer which you may want to explore.
In my opinion, if you are trying to transfer deleted BOM manually to GTS, then that is an expected behavior however the deletion flag of a BOM should be transferred automatically to GTS via change pointers.
Please check if you have an entry created in table BDCP2 once you mark a BOM for deletion in ECC and if this entry if processed from the table after BD21 or RBDMIDOC.
This may help you to understand where the issue could be.
regards,
Kul Vaibhav