I was kinda hoping someone else would answer this. LOL.
Unfortunately, the situation could be anything and this is vague. Since you apparently have not had an accountant handle the books for this "merger," I'm going to assume it's a small company. In which case getting stuff from one set of books to another could be relatively simple. But you're only asking about the loans. Everything from the one company's book should have carried over to the other. i.e. all the assets and liabilities, the difference of which is the equity (or book value or net assets or whatever you want to call it) that would come over to the new company. Meaning the loans would have come with it. It's appearing as though you may not have done this. If you had, you would have taken those loans with everything and they would simply now be included in the new company's stuff.
So without knowing what you did or didn't do already, and how you did this "merger" could make a difference in what you need to do now.