First try to make sure to clear all cache from your browser. Then try again.
When you make changes take a look at your files affected on the server. Have they been replaced with the new amended files, or are they the old files? If they are the old files you may try (after making a backup....important) deleting the files you are trying to update. Once done then try and add the revised new files. Named exactly the same of course. If your site is quite large and it will take some time, then a alternative index.html / index.php page with "Sorry site down for maintenance" may be a good idea whilst you sort it out.
I used to sometimes have this problem. Very infuriating at times. But if you are still stuck a failsafe method is to go into your file management and you can upload a file (one at a time I think) from there.