When you update your server code, you also have to make sure to update all of the required SQL changes to be current as well. I am surprised your server would start at all without doing that.
Yeah, you basically just overwrite anything existing in that folder with the new files. But, if your server isn't having other issues after doing that, then maybe you didn't do something correctly. Those quest commands shouldn't require any SQL changes for them to work, but the server itself definitely will. If you are starting with a fresh PEQ DB, you can just update to the latest one by using their new SVN as described on their forums. If you are using a database that you have already made some changes to, then you will want to update all of the SQL updates yourself. You can find most of the SQL update stuff mentioned in the changelog.txt file. Just start from the date where your server code was from before and read upwards and add the SQL noted in each change in chronological order.
Either that, or PEQ may have more updated server packs, but I don't really know much about that as I have never used them.
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