Recently My work lightroom catalog has been acting stupid. We keep all our images on a network drive and all out photographs are kept in chronological order. I have been working in a folder called 09/28/2016 I have been editing and saving images back to the directory "Round trip" Normally when i save a PSD it appears in the catalog right where it should be. I color it purple to indicate its my Working layered file and so on. Yesterday i noticed a few of my recent edits weren't in the catalog so i right clicked the Date/folder and selected Sync folder. It said there were 200+ images missing. I clicked ok and suddenly the folder moved out of the main directory and went to the top. The 09/28/2016 still in the directory said 0 images. yet when i tried to move the images back into the correct folder it said they were already there. I looked through the finder and all the images are exactly where they are supposed to be but Lightroom has the folder outside the correct directory. This isn't a huge deal its more a housecleaning problem and looks messy. It drives my boss crazy. This problem has also confounded Adobe. So perhaps one of you have experienced this problem and can offer some insight.
... but Lightroom has the folder outside the correct directory.
I think I know what you mean by this, and I think I know the solution — but could you show us a screen capture of the folders "outside the correct directory" in Lightroom, and another screen capture of the same folders as seen by your operating system? I'd like to be 100% sure I understand the problem before explaining the solution so I don't send you on a wild goose chase.