In the CK if you to File > Create Archve and then click 'Pack Files' it doesn't actually update or even create the BSA. Nor does it update the CKM or BSL.
However if you to "Upload to Steam Workshop" you'll get prompted to use an existing BSA (and/or repack it) or it will give you the window to pack a new BSA. When you click 'Pack Files' now it works and properly updates the BSA, CKM and BSL.
Pretty crappy bug. Glad I've been uploading to Steam before archiving for Nexus

