Oh I get him now. If the .nomedia file exists in a folder containing the folders you have it will hide files in all those directories. For example having a .nomedia on /sdcard will definitely hide the whole sd card media. So ensure the folder you want media scanned isn't preceding the folder you don't want media scanned. Like:
/sdcard/myfiles/mediapublic/photos
/sdcard/myfiles/mediaprivate/photos
These are two folders. To hide media in mediaprivate and photos. Paste the .nomedia file in the mediaprivate directory. If it's photos folder only. Paste it there only. And ensure to remove the file from the folder containing that folder. There is another alternative you can use. Delete all .nomedia files. The folder you want hidden, just start it's name with a dot. Like
/sdcard/.myfiles/mediapublic/photos
To hide all myfiles
/sdcard/myfiles/mediaprivate/.photos
To hide only photos
Remember the .nomedia file is an empty file with no code even if you open it with text editor. It is 0bytes size and 0characters. So forget about editing it