Not sure what you mean by "change the structure".
If you mean you changed the file names and locations of the imported source files, then you will have to relink to them. Go to the Assembly view / Project panel, right-click files whose icons have question marks on them, chose "link media" from the context-sensitive pop-up menu, then at bottom right, click on the "locate" button, then navigate in the new panel to the file (new name and path), select it, then click OK.
If you mean you changed the way the imported files show in the project bin, that's not a problem. You can move things into bins, and sub-bins, all you want, and not affect any timelines that use those files. You can even change the name that shows up in the project bin, and this only shows up in Premiere Pro: the PC's files names do not get changed.
If you mean something else, please clarify, and we might be able to be of more help.