I would imagine if the design/assembly information was broadly available (internally) in the past, there's probably one or several "digital twin" emulations of the craft, or at the very least specific subsystems of it's computing resources.
There must be some kind of analog/simulation of it's software just for proving "bugfixes" before upload, like the coms error and subsequent setting of the "solar system record" for "furthest distance remote code update" earlier this year.
There isn’t a simulator or digital twin for voyager. It has a bespoke processor made with 74* style logic. One guy will puts together a command and they will have a review where the other engineers will try and independently verify it. Then they copy and paste the command somewhere to “run it”. It happened, fairly recently, that the command had a typo that was caught in review, but the “wrong” pre-review command was used and the attitude became off by so much that they lost contact. It was only by cranking up the power at Goldstone that they got a command through. This fundamentally changed their understanding of the largest angle for which they could still communicate with the spacecraft. They just hadn’t wanted to try larger angles before because it was too risky.
