You should not amend until the first return is fully processed and you get the first refund. Then the amended return is only the difference you owe back or get. So you should still get the full first refund and get to keep it.
The amended return will only show the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16. If there is an amount owed with the amendment, it will be on line 20.
