Hi Samir,
Technically, if you have two different ECC systems assignment of BSG to logical systems should take care of things, but in your case as you have same location name in both of your ECC systems, and need two entries of same with different BSGs.
I am not very sure about how system handles duplication, same location with different BSGs.
The error you are getting is because of this same reason, system is unable to differentiate between location 1000 from ECC1 and ECC2.
One possible thing which you can do is assign same BSG to both of ECC systems, this is possible, one BSG can be assigned to multiple logical systems.
Try with this and let me know, if your issue gets resolved.
Rgds
Sourabh