Good question. The Hamiltonian MPO and your MPS (or IQMPO and IQMPS) must have the same "site" or "physical" indices in order to be compatible. This is one of the reasons there is a separate site set object, such as "SpinHalf" or "Hubbard" to keep track of the site indices.
So to answer your question, you will need to write your site set object (usually called "sites" in the sample codes) to disk alongside your IQMPS.
Here is some sample code showing how to do that:
Then you need to read your site set back in before making your new Hamiltonian, and use this previous site set when you initialize (construct) the AutoMPO object. This will ensure that the Hamiltonian has the same sites as your MPS.
If that doesn't solve your problem please let me know and we can troubleshoot further.