Kristi from Braintree here. From a technical perspective, having multiple simultaneous merchant accounts shouldn't be a problem. If you'd like, shoot us some details, and we can see how we can help - email@example.com
Kristi answers you below (No, it's not a problem, at least, one I never experienced with any banks I ever dealt with). I will, however, say this: each bank is different. Trust contracts to define. Beyond that, get second opinions on everything. And then get contracts to back it up. You are dealing with money. Probably a lot of money. Spend the time to understand exactly what you are told. What you assume Braintree said may not be what they mean. And always get a contract.