There's almost certainly byte order+version markers in the header, a "happy path" that just memcpy's the structs, and a "safe path" that does byte order swapping, migrates the old structs to the current format, etc.

You can version the structs/loaders by keeping the relevant header files in their own version subfolders, and copious usage of sed. I've done this in a Django project to maintain support for ancient untouchable clients using an old version of the API, it's pretty manageable.