Cannot get files to transfer to remote side after upgrading.

[lizcan]

I'm quite new to this and until now have not had any problems, yesterday I upgraded as requested and now when I upload files to my server, they get uploaded but I cannot transfer my new folder to the remote side of filezilla if that makes any sense. I'm able to connect and when I upload files, it states it was successful but when I go into my cpanel, nothing is there.
Sometimes the file will appear in the remote side but not in the file it was to go into, Can someone help please
Many thanks
Liz