When I execute the bat file to start my server it is now creating the default "my_server_identity" folder and generating a new world in there instead of using the already existing folder specified as below

+server.identity "Innsmouth_Charnel" ^

The only thing I can think of that's changed is I loaded some plugins. I can't imagine any of them would cause this, but I am also fairly new to hosting a server so I could be missing something obvious. 

I can move the stuff from the old folder into my_server_identity and the world loads up as it should, I'm just struggling to determine what is causing it to create the default folder instead of referencing the definied location

Plugins wouldn't be creating that folder. The only thing that would create that is the server itself, and it creating it means that your batch file arg isn't being passed to the server so likely that your batch file isn't formatted properly. Could you post it here?

D:\steamcmd\steamcmd.exe +login anonymous +force_install_dir D:\rustserver\innsmouth\ +app_update 258550 +quit

curl -SL -A "Mozilla/5.0" "https://umod.org/games/rust/download" --output oxidemod.zip

"C:\Program Files (x86)\GnuWin32\bin\unzip.exe" -o oxidemod.zip

del oxidemod.zip

RustDedicated.exe -batchmode ^

+server.port 28015 ^

+server.level "Procedural Map" ^

+server.seed 31415926 ^

+server.worldsize 4800 ^

+server.maxplayers 100 ^

+server.hostname "Innsmouth Charnel" ^

+server.description "Monthly Wipe\n\nMurderers\n\nRewards\n\nzLevels" ^

+server.identity "Innsmouth_Charnel" ^

+rcon.port 28016 ^

+app.port 28082 ^

+rcon.password letmein ^

+rcon.web 1

goto start

+server.url "www.innsmouthcharnel.com" ^

Could you show the full script with that included as you had it? Use a code block or paste link though please.

D:\steamcmd\steamcmd.exe +login anonymous +force_install_dir D:\rustserver\innsmouth\ +app_update 258550 +quit
curl -SL -A "Mozilla/5.0" "https://umod.org/games/rust/download" --output oxidemod.zip
"C:\Program Files (x86)\GnuWin32\bin\unzip.exe" -o oxidemod.zip
del oxidemod.zip

RustDedicated.exe -batchmode ^

+server.port 28015 ^
+server.level "Procedural Map" ^
+server.seed 31415926 ^
+server.worldsize 4800 ^
+server.maxplayers 100 ^
+server.hostname "Innsmouth Charnel" ^
+server.description "Monthly Wipe\n\nMurderers\n\nRewards\n\nzLevels" ^
+server.url "innsmouth.super-crush.com" ^
+server.identity "Innsmouth_Charnel" ^
+rcon.port 28016 ^
+app.port 28082 ^
+rcon.password letmein ^
+rcon.web 1

goto start

Doesn't appear to have any issues from what I see. That URL shouldn't cause any issues either. I'd make sure the quotation marks are all standard ones though.

will do, thanks. For now I just have it removed and it's working again. I'll worry about that when I actually build up a website for it. 

Cheers