There is nothing special about AutoSPInstaller which would lead to a different course of action. If I understand your situation correctly, one of your servers maybe missing the correct binaries and still part of the farm i.e., shows on Get-SPServer.
If this is the case, I would suggest that you run configuration wizard on that server, disconnect it from the farm first (more care needed if server is part of Search Topology).
How to fix after this point should not affect the farm as it will only join the farm when binaries match. I would not manually install anything from the updates folder and No, you cannot simply rerun the batch file and reinstall the server. You would have to disconnect, uninstall all the binaries, then re-install. At this point, you may be better off starting with a fresh server.
As of AutoSPInstaller making changes, it actually may do that. It depends whether your farm configurations have changed since you have first installed SharePoint. You may want to use AutoSPInstaller to install the binaries, Join the farm, install standard services and features, then stop. That will likely leave a lot to be done, but it will likely not change the configuration of your farm.
It is not a very good position to be and the constraints you have given does not make this task any simpler.
If this is the case, I would suggest that you run configuration wizard on that server, disconnect it from the farm first (more care needed if server is part of Search Topology).
How to fix after this point should not affect the farm as it will only join the farm when binaries match. I would not manually install anything from the updates folder and No, you cannot simply rerun the batch file and reinstall the server. You would have to disconnect, uninstall all the binaries, then re-install. At this point, you may be better off starting with a fresh server.
As of AutoSPInstaller making changes, it actually may do that. It depends whether your farm configurations have changed since you have first installed SharePoint. You may want to use AutoSPInstaller to install the binaries, Join the farm, install standard services and features, then stop. That will likely leave a lot to be done, but it will likely not change the configuration of your farm.
It is not a very good position to be and the constraints you have given does not make this task any simpler.