Multiple Harmony Hubs in HA?

You can. You can connect both hubs to HA through template switches. Then expose the switches to alexa via Alexa Smart Home Skill, or the deprecated hasska. Both are one in the same, hasska is no longer maintained because Alexa Smart Home Skill replaced it. It can control everything home assistant cloud can, it’s pretty much the free version of Nabu Casa. It’s just a challenge to setup. Once setup, you can use normal phrases to command the hubs as long as you name your activities with unique names.

Here’s a guide for the template switches & harmony control. Alexa Smart Home Skill is the final piece of the puzzle.