<p>Has anyone run into issues serializing components into a file and reading them back, specifically in the area where the component vendor upgrades the VCL components.  For example a file serialized with DelphiX and then years later read back with delphiY.  Do the serialization formats change and if so what can be done to prevent errors reading in the componets when upgrading.</p>

Formats will defintely change, as vendors will add features to their components. Serialization simply loops over all published properties and saves them to a stream. When they are read back, each of the properties that is read from the stream will be set back to the component. If the property does not exist anymore, you have a problem. I don't think you can do anything about that besides some basic exception handling.
Best way to guarantee compatibility is to do your own serialization.