You can start the migration after you point the MX Records to Zoho. After you complete the steps mentioned in the Mail Hosting process, and start receiving emails in Zoho, you can schedule migration for users in batches of 10. Since you would have started receiving emails in Zoho, there will not be any loss of data.
The duration of the Email migration will be based on the amount of data you have in your GApps accounts.
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