hi Billy,
I assume you are talking about setting deletion flag in Tcode XD05. This will not delete the BP in GTS but instead it will change the valid to date to current date in table /sapsll/pntbp i.e., the date when the customer was marked for deletion and transferred to GTS.
If you quicky verify one of those deleted ones you will see valid to date as expired. Which indirectly means the BP is expired when it has deletion flag setup in ECC. This is kind of soft deletion.
But if you would like to hard delete the BP completely from the system. You need to use transaction BUPA_DEL. After that, you should also run program /SAPSLL/BP_DATA_CLEANUP to clean up all mapping tables including /sapsll/pntbp.
Above all, make sure there are no documents available in the system for this BP.
Regards
Dhilipan