[SalesForce] How to iterate a loop in a flow

Unfortunately, the flow Loop element doesn't work that way. The correct method is to build a three-part loop, which has an initialization Assignment, a Decision branch to know when to stop, and an increment Assignment to increase the counter value.

As you can see, step 1 initializes Counter to 0, then we head into a decision where Counter is less than 3. If so, we enter the Loop branch, which does whatever logic you like, then adds 1 to Counter. This repeats until Counter equals 3, at which point it continues to the Continue branch.

The equivalent version of this in Apex Code would be:

for(Integer counter = 0; counter < 3; counter++) {
  // Do logic here
}

I'm not sure I understand your requirements, but from what I understand I would start this way :

1. get you object A the way you want, store in MyObject variable
2. get its children, save in a variable objectAChildren
3. delete ID from MyObject, assuming you want to clone it in step 4
4. create Object B, ie cloning MyObject. Id of record Object B is now assigned to MyObject.Id
5. Loop through objectAChildren, name the local variable CurrentAChild
6. Save the CurrentAChild.Id to curChildId

7. update CurrentAChild :

   CurrentAChild.ParentRelationField = MyObject.Id
CurrentAChild.Id = null

8. create the child for B, using CurrentAChild variable as data source

9. update record (object A child) whose ID is curChildId, set YourLookupRelationField__c to CurrentAChild.Id

Your object B has now children : clones of obj A children
Your object A children now have a lookup pointing to theirB child counterpart.