Hi Debora,
For the deletion to automatically reflect in GTS, you may have to add field KNA1-LOEVM-Deletion indicator under the message type /sapsll/debmas_sll in BD52.
I believe, you will have a batch job scheduled for transferring change pointers from ECC to GTS. So, may be this field was missing in message type activation and hence system was not transferring deletions to GTS.
You can check the below link, this gives detailed picture
This will take care in future.
Regarding your existing 100,000 BPs, you can schedule a job for manual transfers.
Regards
Dhilipan