Sure, I updated whole directories with Terminal commands like
sudo cp -r /source/directory/* /destination/directory/
In order for the files to have the right privileges..
And one more - as I refresh the page after logging in by going into the address bar and hitting Return, the page comes up with the message list, but the message list pane comes up very small (like something about only 3-4 messages height), it comes right after simply refreshing the page by hitting Refresh button in my browser..
Weird. I suppose, I`d try deleting it and set up also a new MySQL database. But I have some contacts in my contact list, so I`d be happier to skip this step :-)