When I synchronize one selected file or one selected dir, there is no problem. Synchronization is quick and correct.
But when I select more files or more dirs (multiple selection with Ctrl/Shift) for synchronization, it is very slow. It's because Aptana generate synchronization for all files in project and not for that selected files/dirs only. I can see slowly growing percents of synchro process on right bottom and after generating a list I can see tons of "orphaned" files to delete. But this files are not orphaned. They are only compared in wrong place, I think.