Limitations of Predictive Indexing

MS Support also stated the following:

Also, by default, you may not be able to add columns to indexed columns once the list or library threshold is crossed.

Hence, if you want indices to be created after the threshold is crossed, the only available options is to bring the items below 5000 and create the index. You can then contact us for restoring all the items from recycle bin deleted by a specific account after a particular date and time.

I am sharing some best practices when using 3^rd party tools for data migration. However, as this is not a supported scenario for our break fix team, we cannot assist you on this concern.

Please refer : Avoid getting throttled or blocked in SharePoint Online

To avoid getting throttled when migrating data:

1) Don't retry in a tight loop 

• SPO will charge for the small amount of time/ CPU needed to determine if the usage is over quota.
• If the customer retries in a very tight loop, these small amounts can sum up to make them remain over quota.
• Generally the response headers have a back-off time that tells you how long to wait before the next retry.

2) If users keep hitting the throttle limit, see if there is a way to make lighter-weight calls. If not, implement a wait-and-retry loop.

3) Quotas are by user or app id. If they are not connecting via an app id, use a different user login.