I had this kind of thread few days ago, but that was totally different situation:
Some plug-ins require to be installed in unordinary way - some files to wp-admin, some files to wp-content and so on. So, whereas I updated WordPress to 3.1.3 manually (by just dropping wp-admin, wp-includes folders to ftp), now I have some files in these folders and can't just overwrite them..
I have tried to copy files from these folders and paste in related directories (filezilla offered me to overwrite existing files/folders and I clicked yes of course, because in this way necessary files wouldn't be deleted), and everything is done right now, but filezilla failed to upload some files (3, or 4) and I have uploaded them manually.
System works, but in some places it shows me errors, related to those files, which I have uploaded manually, for example - wp-includes/functions.php when I saw this error, I re-uploaded this file but error didn't disappear (see the screenshot).
So, I have backup of whole system (before I started updating), so if I had made any mistake there isn't big problem, but if it is possible just to correct them, it's much more better of course.
Tell me what to do, please.
Thank you very much.