Also, are you saying that an updated version of ulx from the svn would fix my problem with the bans, or are you saying that I need to start over with a new version and scrap my old bans.txt file?
I'm saying always use latest code, because old code got broke after a Gmod update (totally beyond our control at the time)
As for you 'having no addons that affect bans' has nothing to do with the fact you might have addons that affect writing files properly or adjusting/overwriting other functions ULX uses. (Fadmin is a perfect example of this, we recommend people use the latest of it because earlier versions were much worse about conflicts (and actually, we still often recommend using either Fadmin or ULX, not both)
I'm saying that, since your bans file was considered broken before you tried doing anything, there's a
possibility you've lost it, yes.
Something corrupted it, whether it be due to your download/re-upload, or a bad zig when it should have zagged during a save, or Gmod not writing it properly, or someone with an odd character in their name.
As for your SVN troubles, if your using the zip file as I suggested from the github site.
https://github.com/Nayruden/Ulysses/archive/master.zip - there are no .svn folders in it. at least that i can see, and I have show hidden files turned on. It contains files from every project we write, but, you'd only need to upload the ulib and ulx folders to your server.
There are only one or two github related files, and they should have no issue with them (a readme.md, and a file called .gtignore.