Change Property of db.Model to custom Type
Its not sql. You dont clone or delete 'tables', no such thing in the datastore.
To do the migration you would use task queues to run through a query. You probably need to stop your frontend while doing so. Task queues have a longer limit than the 60sec you mention and each taskqueue will  create another one until you finish pro essing all items in your query.
Yiu also complain that its harder than other enviroments but it isnt so. The problem maybe is that you chose to use the datastore instead of cloud sql which you could also have used. Each has its pros and cons.
I'm trying to change the Property several Fields on my GAE AppEngine to a custom Type (Encrypted Content).
Most of them are currently String or Text Properties. Since we have multiple millions of Entries in our DB, migration is not an easy task. I'm looking for a best practise, here is what I think will work best but this might be very challenging to execution time limits plus I'm a little bit frightened about the costs for this task.

clone table to tmp_table
delete table
create table with new attributes
insert values from tmp_table into table

What sounds like a short hiking trip on most environments feels a little bit more complex on GAE ;)
My Questions to you:
- Are there any know best practises you are aware of / did you already achieve this challenge & how?
- Any Idea how to trigger the process (I would estimate it takes several minutes so the 60 second limit