You could, perhaps more simply, add a feature a bit like extensions, where Construct can look for a plugin which explains how to convert an old file format to a new one. So in a simple example, if the file header now includes a bunch more stuff, the plugin would read the old file format and reorganise it into the new one.
I'd have thought you could use your file-reading code from the old version, and file-saving code from the new version, to lift everything into memory, then shove it into a file using the new routines?