This has been discussed many times. With many third-party integrations, including Ifttt, Alexa, Google Home, etc The integration is at the account level, not the location level. So when you have more than one hub, it just gets pretty random as to which devices will be exposed to the third-party integration. It might be from one hub, it might be from the other, it will not be everything.
There’s nothing you can do about this, smartthings has been aware of it for three years now and they just keep saying that they hope to change it in the future.
So you need to have not just two Ifttt accounts, but also two smartthings accounts. Otherwise you are out of luck.
Here’s the comment on echo, but it also applies to Ifttt:
Can I control multiple SmartThings Locations with Alexa?
No, not at this time. But we are working on an update that will allow multiple Amazon Alexa devices on separate Amazon accounts to control separate SmartThings Locations.
Like I said, don’t get too excited about the “we are working on it“ comment, that’s been there for three years.