Vijay,
We handled it as follows:
1. Developed a BDC to upload project for CJ01 and CJ02 T-codes.
2. The ACL is already activated in configuration and hence, the user ID using which projects are uploaded becomes default Admin in ACL.
To update this -
3. The code in the upload program was extended to include ACL deletion program CNACL_DELETE (T-code: CNACLD)
4. Create ACL migration program as per Note 1239943 - Activating ACL in existing projects and pass on the required ACL details to the newly uploaded projects.
Trust this approach helps in your situation.
Regards,
Rahul