When you already started to replicate or upload master data from one system you should not delete this system any more. If you do so the existing master data will loose their source system and you cannot reassign it by recreating a system with the same ID.
The reason is that every system has a GUID (globally unique identifier), which is not visible on the UI and if you delete the system the GUID is gone. if you recreate a system with the same ID it gets a new GUID and the existing master data still refer to the old GUID.
Instead you can change the IDs and technical settings of existing systems or set them to obsolete.