Hi Ian,
Generally speaking New GL can replace PCA. That's why usually you will switch off PCA after activating New GL. Only the Profit Center as master data object will remain and shall be used as characteristic in New GL.
As a consequence, you can deactivate the PCA transaction data flow(s) in BW at some point in the future. Especially if PCA is switched off in the ECC system, it won't make sense to continue loading from PCA. You must continue the Profit Center master data loads.
Best regards,
Sander