Just replied to your email but also gonna post the answer here in case anyone finds it useful in the future.
First, I’ll note that nothing (including plugins) can alter version history (unless there is a serious glitch in Figma). So if you restored a file, it should be restored no matter what modifications the plugin did to it.
Second, let’s say you “Pick target component” in File 1, then go to File 2 and “Link objects to target component”. Then you click “Go to main component” when the instance in File 1 is selected — no access. Same in File 2. When Figma says “You don’t have access to this file” — it means you don’t have access to the file which stores main components (the file is closed by the owner, you are not invited as a viewer or editor). If you can still open that file and can confirm that the components are the same as instances, this is a bug in Figma. You can only do that via plugins API. Install the Node Inspector plugin and check if “key” property is the same on main component (component → key) and on instance’s main component property (instance → mainComponent → key).
If component keys are indeed the same and you do have access to the main component file but Figma says you don’t — this is a never seen before bug in Figma, you can report it to Figma support team. But first check if simply restarting it or logging out and back in would help. If that’s not the case (if the keys are different), the file you think stores the main components is not the file that actually stores them. In this case, as I said above, you just don’t have access to the file where they are stored.
If this doesn’t help, I’ll probably need editor access to all the files in question to investigate, or we can have a call sometime next week or this weekend so I can give you more clear instructions. But in any case this sounds like more of a Figma issue than something wrong with the plugin.