This definitely happens if you choose a different directory than CC4 is expecting when importing the textures. You might have chosen one level too deep, or not deep enough, on that dialog.
For example, let's say you choose "Export Character to Substance Painter", and you export the character as "MyCharacterExport.obj". You bring that into Substance Painter, and you texture everything, and export it to a directory named "C:\Temp\SubstancePainter\Export". Now if you look in
C:\Temp\SubstancePainter\Export, you'll find a directory with the same name is the .obj file you initially imported:
Back in Character Creator, choose Update Textures from Substance Painter, and choose that specific folder (the one with the same name as the Obj file), then press Select Folder:
Don't simply choose the "
C:\Temp\SubstancePainter\Export", or one of the directories within "C:\Temp\SubstancePainter\Export\MyCharacterExport". You need to choose "C:\Temp\SubstancePainter\Export\MyCharacterExport" exactly. Assuming you do that, and that you remembered to export from Substance Painter with the "Character_Creator" export settings, it should reimport into Character Creator correctly.