Boot into your custom Recovery, mount the data partition either using command-line or via GUI, and choose any of the following method:

_{(Note that TWRP already has the option to clear /data without touching /data/media. It uses rm -rf commands¹.)}

Go Immune

1. Make /data/media immutable² i.e. immune from any modification. You can do so by executing:

   
   
   

   adb shell chattr +i /data/media
   
   

   
   
   

   You can also use -R for recursive immunity, though it was not needed in my test case.

   
   
   

   You can see the immune attribute (i) in the output of

   
   
   

   adb shell lsattr /data/
   
   




2. Time to go berserk

   
   
   

   adb shell rm -rf /data/*
   
   

   
   
   

   All the files and their holding directories inside /data/ should now be purged except the ones inside media, for which you would get the error (non-critical) Permission denied for every file inside that directory.




3. Now revoke the immunity using

   
   
   

   adb shell chattr -i /data/media
   
   

   
   
   

   Use -R if you used it previously.

If-Else

Manually pick each directory under /data and use rm -rf on it. Could be tiresome, so you may consider Izzy's shell-fu

adb shell for dir in /data/*; do if [[ "$dir" = "/data/media" ]]; then continue; else rm -rf "$dir"; fi; done;

Replace rm -rf with echo for a dry run.

The command picks up each file-path³ under /data, then checks against whether the file-path is for media folder: if yes, then pass; else nuke the file.

<sub>1: TWRP FAQ: What is a data/media device?

2: Wikipedia: chattr

3: General overview of the Linux file system: Sorts of files</sub>