You can only transfer the employees you need to the bigger base without it counting as a layoff at the one you want to close.
What I would do is:
1. make sure your personnel setting is manual (don't auto-hire)
2. close the smaller base. All employees are automatically transferred to your HQ
3. as you grow your other base, transfer employees to that base from your HQ as needed using the "transfer between bases" feature on the personnel page