After reviewing the usage of gDoNotReloadFiles in files.e - I see that if I close the file and then reopen it, that I can get warned again. I also see this from re-reading Patrick's earlier post. I think this may have been happening. In the case of this log file, if I close it and reopen it, I really do not want to be notified if it was modified outside the editor - I know that is happening and I have a bound key to refresh the file when I want to. Also I have multiple files with the same name (but different directories with the date in the directory), and I may have been getting prompted for those and gotten confused. I will monitor it more closely for the future.
Is the behavior for removing it from the list upon closing the file new for version 23? I think that in v22 if I close the file and reopened it, and if I did "Never reload selected" before closing it the first time, I would never be warned about it again. Sometimes I have too many buffers open and do a File->Close All and then later I reopen this file, so this could have been happening.