To answer your first question, at the moment the file formats used by ITensor are not guaranteed to be stable to version changes, due to the fact that we write out the binary representation of objects in memory. So they are also not guaranteed to work across different machines with different binary formats. So it's still a useful feature for writing objects to disk and reading them back throughout a single calculation or within the same version of ITensor, but not meant as a long-term storage solution.
One feature we are planning to add after we first address some other things is to add support for HDF5. Then we can have long-term stability of ITensors written to disk.
To answer your other question, I think you are right that combining TagSets and Index's in the prime function doesn't currently work. So as a work-around for now, please just call prime twice with the different arguments you would like to use and that should work. But also could you please file an issue about allowing this combination since I think it would be straightforward for Matt to add it.