How Regenerators work
As I mentioned before, thanks to the Foundation, this setting has access to "Regenerators", enormous machines that can bring thousands of people back to life if necessary. Smaller regenerators also exist, though they're slower and can't resurrect as many at once.
The way this works is that people imprint a "Save State" of their minds into soul gems, which are then uploaded into the Memory Repository, usually before a mission. If the operative dies and their soul gem remains intact, it's possible to extract a more up-to-date version and bring that back.
Then they simply give the Regenerator the brain-pattern imprint and medical records, and it spits out the once deceased person. Well, growing the body takes some time, but it's not that bad.
There is also a pretty infallible system to detect if a person is still alive, and if someone was to get doubled, the system would quickly stop recognizing the double as a double and give it the status "nth childof" with a link to the original person. Though the Foundation tends to avoid making doubles in the first place, they might cave in from enough pressure.
However, in one of my battle scene drafts, Captain McKenna is with a dragon and a gryphon, trying to get to their mission objective. But then they encounter his old "friend". After McKenna quickly sends his squadmates away, we get this line from old friend:
You were never one of us. You are nothing but a usurper, a false idol. My eyes have been opened. Let me help you to see, Captain. And this time, you won't be coming back anytime soon."
The gryphon and dragon finally get to the other captains and tell them what they saw. The other captains go full panic mode and rush to McKenna's aid.
So, there is a way to delay someone's regeneration for long enough to cause serious problems. This time varies but can be as long as 15 years. Furthermore, if someone's regeneration gets delayed, there's nothing the Foundation can do about it.
We know that McKenna's old friend (and anyone else for that matter) can't screw with the Foundation's regenerator, or the Memory Repository that already has an older instance of McKenna on it, and a compromised/hacked soul gem wouldn't go unnoticed during debriefing.
So how could a person's regeneration be delayed (but never completely stopped) reliably without messing with either the Regenerator or the Memory Repository?