I don't know all the details. But you only need to check the linkings once. And as I said, there is also the check linking properties tool in openLCA. Also what I mean with checking an ecoinvent process is that if you get the same results in the ecoinvent library and the ecoinvent database (which you should), the reason for your differences are most likely in your own imported and exported foreground processes. And a copied and modified ecoinvent process is also an own foreground process. Only what is immutable in the ecoinvent library counts as background.
I will test the transfer for bugs, since I don't use the ecoinvent libraries often. But I understand your use case that you want to create an immutable, error proof tool. By the way, you can also transform any database that you want, also your own models or full databases, into a library by yourself. This functionality is in openLCA. And with one of the next versions of openLCA, there will be also a migration tool included, which makes migrating own processes from one database (even if different ecoinvent version) to another much easier.