The best way to proceed a Migration from Website 1 to Website 2 is to use the Cloud module where you don’t need to download/upload any file and just to connect both websites on the same online Destination
Are few main steps to follow:
1) Website 1(Source)
- Set an online Destination (FTP, DropBox, GDrive, etc)
- Create a Snapshot with what you need (if you wanna the entire MultiSite, check that)
- Check the Logs to see that the Backup is done
2) Website 2 (Destination)
- Go to Cloud tab
- Set a Cloud Destination (NEEDS to be exactly the same as destination set on Website 1)
- Go Back to Cloud Tab (you will see a new box with your Snapshot from Website 1 )
- Click on “Cloud Migrate”
- Set your preferences and proceed your Migration
Be sure that on both websites the backup and migration processes can be handled by your server and are not stopped during the process time. You can have a first test with only few data for migration (such a DB table or plugin).