When I start my Rust server Oxide is running, oxide.version responds with 2.0.4879. (odd, considering I just downloaded 2.0.4973). However, when I add new mods, and relaunch server, the config files are not being created. I also noticed that the log files (RustServer\Oxide\Logs) are not updating either.
An old post in umod forums mentioned to remove the oxide.config.json file (while server is down) and start up again. Indicating that the config file would be re-created. The file was not created when I launched the server.
I have updated Rust, and then downloaded/installed Oxide again (both over the same existing folder), but still having the same issues.
I modifed NTFS permissions giving the computers local Users group all but Full Control of the Oxide folder (and contents), but still same issues.

I resorted to deleting my RustServer folder entirely and going with a fresh install.

1. Deleted my RustServer folder.
2. Installed Rust (258550) from SteamCMD.exe to C:\RustServer
3. Launched Rust. Once it said Server Connected, typed Quit
4. Downloaded the newest Oxide from https://umod.org/games/rust
5. Unzipped, then copied the Oxide RustDedicated_Data into C:\RustServer (selecting to overwrite everything)
6. Launched rust and waiting for "Server Connected"
7. No Oxide folder.
8. Quit server
9. Launched server again, this time the Oxide folder was created.
10. Added plugin and typed oxide.reload
11. I got the config files.
12.  Everything seemed good to go. Joined the server and it was working.
13. Typed quit to stop server.  Started it up a few hours later.  Same problems returned.
- Oxide.version responds with 2.0.4879, even though I downloaded 2.0.4973
- The Oxide log files are not updating
- Oxide isn't reconizing any plugins. When I try to assign permissions it doesn't know plugin is there.
--- Oxide.reload whitelist - Could not load plugin "Whitelist" (no plugin found with that file name.
--- Oxide.load whitelist - Could not load plugin "Whitelist" (no plugin found with that file name.
- If I try "oxide.reload *" it just hangs and does nothing
- Restarting the server so far hasn't helped.

Windows 10 (20H2)
Intel i7-3770
24GB RAM

I do have dedicated Valhiem and Conan Exiles servers on this same computer, but even with those servers stopped I still have the same problem.

We would need to see your oxide/logs or the server log.

Sorry, dumb question.  Where are the "server" logs?  Wondering if may be I need to enable something.

I checked in C:\rustserver\server\my_server_identity and found only one txt file.

Checked in C:\rustserver\logs. There are a few txt files, but none seem to give details as to what the server is doing.

Edit:  OK, this is quite odd.  I added -logfile C:\RustLogs\gamelog%dt%.txt to the end of my rust batch file.  I've launched Rust twice, and both times Oxide seems to be working properly now.

It'd be the file under your RustLogs there.