You have migrated accounts using the activity Migration of Customers . The ID mapping for Accounts is saved under ERP Accounts instead of Business Partners.
Reproducing the Issue
1. Go to Business Configuration workcenter
2. Select Implementation Projects.
3. Select Open Activities list
4. Search the activity Migration of Customers
5. Select Migrate Customer using the migration tool
6. Select and Execute step by step migration
If you have Intergration scoped in the system, in this case when you are migrating the Accounts the mapping will go under ERP accouts.
Since the information is considered from Accounts and External ID is already passed into the Accounts.
This is expected system behavior. If you want the External ID to be under Business Partner then you can Import it using Excel which is available in the ID Mapping for Integration.
KBA , LOD-CRM-EMP , Employee , How To