Hi,
Just recheck and follow below steps.
1. First load all data form source system.
2. Cross verify at SMQ1/LBWQ/SM13 and RSA7 at source side, it needs to have 0 count.
3.Delete the source system assignment by using BDLS or table RSLOGSYSMAP. You can removed old source system entries.you can take basis team help.
4.The process chains which are pulling data from old source system, you can delete or Keep them on hold. Same chain can be reused by changing the source system. its upto you.
5.You can delete the source system assignment from bw. Go to RSA1-->tools-->Assignment of source system to source id and conversion of logical systems.
Thanks