It is better practice for transparency to do the update of your model from on older ecoinvent database version to a newer version manually. We will provide a written guideline on how to update a model. The reason is that from one ecoinvent version to another, a few processes could be missing, or names (links, maybe reference flows) have changed etc. The script would act like a "blackbox" if you have not created it yourself.
The good news is that the manual update is quite straightforward, since openLCA gives you an option to check for missing providers in your new database. And missing providers (from the background database) can only appear in your own foreground model. It is also possible that there are no changes, depending on the size of your own model. You can select a new provider by searching the old one and making a reasonable choice for the new one.
With the guideline and with your own update routine, you will directly know why you needed to change a provider in the newer version and you can track which provider you changed in the newer version. And be aware (referring to your old messages) to better not mix (importing) different ecoinvent versions in one, single database. Keep them in two separate databases in openLCA. And be aware that you cannot update your model to 3.9.1 in case you used APOS in your older ecoinvent version. The system model APOS is not yet released by ecoinvent for version 3.9 (or rather 3.9.1).