I have a CF 2021 server that's had some weirdness installing certain updates. For that reason, I've uninstalled all updates, by running the uninstall file on the cmd line. Now it says it's on update 2, with a bunch of updates it wants me to install, which is where I want it to be. However, when I try to install updates 3, 11 or 12 (all I've tried), it says it's already installed. What would folks suggest from here?

Just to double check Dave, did the uninstall delete the hf-2021-000xx-xxxxx update directory and associated .properties file? If not, do that and run the update again.

Server was stopped during the uninstall, so inherently got restarted. Directories for 5 updates are still there, like hf-2021-00003-329779, might be the ones that were separately installed. If you're uninstalling from the cmd line, do you need to manually run all prior uninstalls?

No, but if you're reinstalling HF 5 (for example) after having uninstalled it, you should ensure that the directory and .properties file for HF 5 have been deleted before doing so.