Hi,
if your new and old source systems have same data then bw will holds duplicate data if you load full load from new source system.
You need to discuss with your users and take proper actions.
If two source systems have same data then you better to load data from any one server.
try to avoid duplicating old data in bw.
Use source system specific. mean use 0logsys info object to know data from which source system.
if your facing some issue please explain more details about issue.
info object master data deletion is not mandatory. if we reload same data, it will overwrite the old data.
At cube level need to do deletion if same data loads from new server.
Thanks