Hi @TKaney,
The best way to do this would be association labels, Then, you can label the associations appropriately to help you identify other companies that they should be the primary contact for. You’ll probably have to update any automation to utilize the new labels to avoid scenarios like the one you mentioned here, where people are receiving errant emails. Overall it should be a little more complex but not too bad.
Also wanted to mention that Insycle (full disclosure, I work for them) allows you to update associations with labels in bulk, which might be helpful to you here. Here is our help center documentation on this. You can bulk update existing associations based on rules, or even inject them into Workflows so that the associations happen automatically after new records enter HubSpot.