Well, sorry, but it sounds like an unnecessary hassle.
It should never normally be needed, but in this case, the previous album upload must have been interrupted abruptly
Any simple FTP client will ask you what to do with existing files, and has an option of overwriting just the older files with the newer - that's how any file managing program should work in my opinion - this security feature makes things just more complicated and underestimates the average user. A smart dialog would do the trick. Why else would you want to upload files, if not to update an album?
I'm just using Filezilla for now - just faster...
Trust me, we've had too many users accidentally overwriting files. By having them manually delete "index.html" or everthing in the target folder unless there is already a jAlbum album in place there, we have cut these accidents to zero.