Ground loop Isolation transformer, alternative

First, there are no such things as DC transformers. Transformers inherently work on changing magnetic field, which doesn't change if you put DC thru it.

What you are asking for is called a "DC to DC converter". There may be modules you can get that do 1:1 with isolation. You'd have to look around.

However, this smells like the wrong question. It's a bad idea to ask about a particular solution you've decided on for whatever reason. If you're asking, you probably aren't aware of the various possible solutions. Explain what you are really trying to solve.

It sounds like you have a ground loop problem. There are various ways of attacking them, with a DC to DC converter not usually the best answer. If you've got two separate things to power, why not just use two power supplies to begin with? What connections go between the two units? How far are they? What are the nature of the signals? Can these signals possibly be transformer coupled, or opto-isolated? There may be other ways too.

Step back and explain the real problem.

Normally this would only need 4 wires: the common, and taps for the three voltages. Having 6 wires complicates things a bit.
One way to find out is to measure resistance between wires. If there is indeed an common and three taps you should measure \$\dfrac{220}{120}\$ the resistance between 220V and common, compared to the resistance between 120V and common. So look for ratios \$\dfrac{220}{120}\$, \$\dfrac{250}{120}\$ and \$\dfrac{250}{220}\$. If you measure a relatively small resistance between pins, you're probably measuring between 220V and 250V.

Alternatively you can apply a low AC voltage (from the secondary from another transformer) to the secondary and measure voltages between pins, and find out the ratios. Even if you know the secondary's voltage and apply that, don't expect to measure 120V, 220V and 250V, since an unloaded transformer outputs higher than nominal voltage.