Hi Marco,
The fact is that UGENE settings do not affect project files. I mean, if you downloaded some PDBs, stored them in ~/UGENE_downloaded and saved the project which contains these files - the only way to change the project is to remove such documents and add them again from another place.

Path do downloaded data stores the path where _new_ documents will be downloaded. Changing it won't affect your existing project and its file structure.

Marco, I suppose that the good (and quite common) solution is to store not absolute, but relative paths in project files.
With this approach users will be able to move easily the whole directories with projects. I think that we will schedule this feature to one of our nearest releases (1.6 or 1.6.1).

But I still think that it is not appropriate to search files stored in project in directories specified in the settings. User may have many files named equally, so if the one stored in project was occasionally removed another document, but with the same name will be loaded from 'downloaded' folder. As I think it can be a rather confusing behavior sometimes.

Such conception is good with some 'global' data, such as UGENE plugins, script adapters, SITECON profiles or something else, but not with regular user documents.