From the symptoms that you're describing, I'm guessing that you have your server configured to look for file modifications, and to load the new file when it has changed, rather than requiring a sysadmin to kick the server to look for changes. (I'm not an FCGI user, I use mod_perl, so this may be the defaults under FCGI, for all I know)

If this is the case, I would advise against FTPing directly over a file. Depending on the time resolution of the engine that tracks file modifications, it may notice that the file has been changed mid-upload, and then not notice that it's been further changed when the upload finishes.

I typically upload to some alternate location, and then move the files into place. (if you're using FTP, use the 'rename' command)

I would also suggest looking at your webserver logs, and seeing if there are any more details about the 500s in your error log.