See in your case i am assuming this as a fresh initialization as you are refilling the complete setup tables so delta records are of no importance in my eyes.
As soon as you lock the users,so no transaction will happen and when you fill the setup tables it will capture all the till the time user was locked.
Now sooner or later when setup is fill,you can initialize the package in BW side so that it creates an entry of datasource in RSA7.After that you can unlock the users..Now the newly posted records will go
into base tables as well as LBWQ..
With the help of V3 job records can be pulled to RSA7 and then you can continue running the delta package.
Hope this makes sense.
Regards,
AL