Which system model and which Nexus release version of ecoinvent 3.11 are you talking about?
The latest Nexus release from 31.01.2025 should have random and different UUIDs numbers for processes in the system process databases so that it can be merged with the unit process database. However, I would still suggest to only use the unit process database, since copying, backups or searches will be much quicker and there is very few arguments to work with the system process version alone or combined.