I try to figure how thats works ...

Basically, i know that the smart upload/download compares timestamps and file size ... but the main problem that i have is when i delete a file on the local disk and i choose smart upload/download, phpEd download again the file recently remove ...

Maybe i do something wrong or is that normal ???

Say, you have nothing on your workstation and clicked smart download, probably you'll expect it to bring you all the files. Right? How to distinguish situation when some local files were deleted for a purpose or by mistake? We decided that in this case it's safer to download vs skip.
On the othwe hand, what you asked about makes sense too. I think we'd think of another function, like "smart merge" that will delete files on destination that do not exist on source location.

dmitri,
I'm frustrated with the same issue. Are there any plans to implement a "smart compare" in the future? As it stands now I have to keep another ftp program open in order to delete files on the remote server. seems rather inefficient. couldn't you just open a dialog confirming that "filexxx" will be permanently deleted from the server when you do a smart upload?

Thanks,
Keith

I agree, it would be nice to have "smart merge" in PhpED

I totally agree this quote ... or a simpler approach is to synchronize the remote and the local workspace ... Dreamweaver works very well with that. Maybe easier to implement than the merge.