This is Dallas from the Shopify Social Care team.
That is an interesting situation that seems to be happening. They technically shouldn't have trouble connecting since there are two Facebook accounts and two Shopify accounts.
When it comes to Facebook the amount of support that I can provide is honestly quite limited. Even though the Facebook sales channel is connected to the Shopify Admin, Facebook is ultimately the team that would need to be contacted about this request because they have full control over their channels for support.
I don't normally provide support for things like this, but I did want to give a few notes. You said that you found that one account was able to connect when you disconnected the other. With that said, my first suggestion is to disconnect both accounts on both stores and reconnect each store with their respective Facebook account on the incognito browser. It might help to connect the accounts when you're not dealing with backed-up cache and cookies. I cannot guarantee that will work, but based on the problem you're having it might be worth a try.
The other suggestion is to give you this link that sometimes goes through to Facebook support. It's honestly very hit or miss as Facebook doesn't have a lot of on-demand support, but I think it is worth a try. I wanted to share this because it's a hard link to find so when you contact the Facebook Forums for the support you might not see it.
I know this isn't what you're looking for in any way shape or form, but I truly truly hope that this helps you a little bit.
Best of luck from your friendly Shopify Social Care Team,