If you mean to turn any individual molecule directly into any other one, then likely no, because the first molecule would not have the exact elements required to make up the final one, and also, there’s no method available to manipulate individual molecules like that.

If you mean to convert a reasonably large amount of one molecular substance to a reasonable amount of another one, then yes, since you could always break it down fully into constituent atoms and then use the methods that were required in the real world to create the target molecule. But then you would just be synthesizing the final molecule from scratch, without really any reason to call it “made from the first molecule”, especially if other new components are required and/or others that were present in the first molecule are not required.

If you mean if there’s a process that goes short of complete breakdown of the first molecule? Probably not for every possible input/output pair.