This is the answer from support team, hope it helps others:
Currently, Dialogflow doesn't provide a default feature or shortcut in the developer console to put the follow-up intent to a parent intent by uploading JSON files. But you can always achieve this by exporting your agent as a zip file and manually add the "parentId" ("id" of parent intent), "rootParentId" ("id" of root parent intent) fields in the JSON file of the follow-up intent and restore your agent in the developer console with the modified agent zip file.
Unfortunately, I don't believe there is a way for a user to move a follow-up intent to another parent intent. It's also not possible to transition a top-level intent into a follow-up intent.
You can export the total dialogflow agent data, and modify the json files in the "intents" folder.
And there, you will find these values and modify the parentId and rootParentId according to the parent intent's "id". Then recompile the zip, Delete all intents, restore using the modified zip file.
{
"id": "c6f2883a-aa05-46e0-af0e-58dc96ebe7a0",
"parentId": "21e013a7-091d-40e4-89be-1d6a842d7fd6",
"rootParentId": "21e013a7-091d-40e4-89be-1d6a842d7fd6",
.....
}
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