Xcode can't find source files

I'm using Xcode 8. I recently inherited a project with several hundred files (including source and image files). I rearranged them on my local drive and the file names (appropriately) become red in the folder list on the left side of Xcode. I selected files/folders in this folder list, click on the "Hide or show Utilities" button to display the "Identity and Type" pane on the right side of Xcode, clicked on the little folder icon next to the Location, and selected the files'/folders' new locations. The text in that pane was updated to the new location and the file/folder names changed from red to black. So far, so good. I did this to all of the file/folder names until none of them were displayed in red.

However, when I go to build the project, I get numerous warning messages similar to, "image.png /Users/Me/Project/images/image.png is missing from working copy." The path shown in the error message is the file's OLD location. When I look at that image in the file list, it is displayed in black. When I select that file and look at the Full Path in the pane on the right, it shows the file's current location (e.g., "/Users/Me/Project/images/newfolder/image.png"). I'm unsure where in the project the old location is being stored. FWIW, I've tried Cleaning the project...

Thanks for insights.

So here is an approach that is perhaps not for the meek, yet it is something I do more often than one would expect to fix Xcode project files. I tend to be the one designated to do this on the teams I work with ... manually editing the project file. The .xcodeproj file is really just a special folder. The actual project file is project.pbxproj.

First back up the project file. Your choice on if you want to do the complete .xcodeproj or just the project.pbxproj.
Use your favorite text editor and open up the project.pbxproj file.
Search and replace the prefix to your path. For the sake of this exercise, you should try and keep your path as similar as possible to make it easier. For example, if the hardcoded path is /Users/Me/Project/Images/newfolder/image.png and all prefixes are generally "/Users/Me/Project", you can just do a search on "/Users/Me/" or "/Users/Me/Project" (the latter if you want more safety) and replace with "/Users/You/" or "/Users/You/Project". Note I am not searching on "Me" and replacing with "You". You want to search and replace but as controlled as possible.
Once done, save and open the project. If the project doesn't open at all, it means you messed something up. Start over. Note that changing the paths should not be sufficient to break the file. It will probably mean you accidentally added or deleted something.
If the project file opens now build. It should hopefully build.

Okay, so that gets you into a buildable state. Now you really want to fix things. Whomever did the project was a knucklehead for using absolute paths.

This next part will be tedious. There are probably ways to do this manually, but I'll leave that to an exercise for the reader right now. In file inspector within Xcode, you will want to change files to be anything but "Absolute Path". Here is an example, you can see the location is "Relative to Group".

Essentially you are going to have to around to Groups and files and fix things up to not be absolute. Make sure you backup incrementally and can build.

Wait, but unfortunately there is more. You'll then need to go into Build Settings to see if things are absolute paths. Then you'll need to decide how to adjust for that. For example, it is not uncommon for 3rd Party frameworks to be added with absolute paths.

Or I suppose if you want to, you can just get it working and skip the latter part of this and damn everyone else...