Sometimes, new features added to Designer require that the Substance 3D file format (SBS) is updated to support them. The user is prompted to update the file when loading it, but the original file is left unchanged until it is saved in Designer. After saving, the file is not backwards-compatible.
We understand this is inconvenient for the reasons you mentioned. Our recommendations for managing this limitation are listed under the Application is too old to open URL section of this page. We do not have plans to share yet regarding backwards compatibility, and I appreciate your patience.
I will make an addition to our documentation with a list of file format versions and associated minimum versions of Designer which support it, as a reference for facilitating collaboration across teams.
Luca Giarrizzo | QA Analyst, 3D & Immersive | Adobe