linux web server centos 4.9 (strongbolt2) with bluequartz web gui

I have a website on the server that is showig excessive disk space usage. Every day I get a warning from the server that the site has exceeded it's quota of disc space. The space allocated for the site is 50Mb. The actual space used so far is 2Mb, but the web gui says the site is using 526Mb. In the console I've been through all the folders for the site and users several times and there are no big files anywhere. I've tried deleting the whole site and all users and then re-creating the site but the error comes back. In the bluequartz web gui under sites system disk usage the service named is "Usage Logs 526Mb". This is a command-line-only machine so how can I find where this huge file is?

well what's the quota data based on? Presumably it is the dedicated user account that owns those files? So there might be files elsewhere owned by the same user. If you totally delete that directory then it must be elsewhere, outside of that, the only other thing sounds like a few nasty dotfiles, so what about "ls -la" in that directory?

the quota is based on the disc space allocated to the virtual site when it was first set up, which was 50Mb. The virtual site in question has one user but there aren't any reported problems with the user side of things, it's the site itself that is the problem. I'm baffled as to why the Uasge Logs are reporting 526Mb used. I also did a search for all files over 500Mb in size and every file found was legit and not connected with the site. what's a dotfile?

"Usage Logs" may well mean 2 or more files totalling 526 MB.

Find where web logs are stored and have a look.

And do a search for all files owned by the username in question.

most logs are in /var/log but I could find nothing in there about site disk usage.
I deleted the site again, deleted any and all remaining folders for the site and then restarted httpd. I then recreated the site without a user, so it was just a new empty site and the usage logs still showed 526Mb used, so it's not a rogue big file, it's a remnant/leftover entry in another file somewhere. problem is I don't know what file or where it is.
what would be good is if there was a way I could wipe ALL usage stats and make the server start over again. I have no use for the existing stats anyway

You could "apt purge" or equivalent to clear logs and stats.
What daemon are you using?

I don't know what daemon controls the usage logs but I'm using centos 4.9 as the base OS. Apt purge sounds like ubuntu, is that right? if there is an equivalent command for centos I'd love to know what it is. I did a search on google for this but couldn't find anything.