The partition should be empty, except for a couple of directories, are you sure that the partition is mounted?
ssh to your router and type this:
cd /jffs
find
it should list some dirs, but that's it.
admin@RT-AC87U-1C70:/jffs# ls -ltr
drwxr-xr-x 2 admin root 0 Jan 1 00:00 configs
drwxr-xr-x 2 admin root 0 May 13 11:30 scripts
-rw-rw-rw- 1 admin root 86064 May 13 12:30 syslog.log
admin@RT-AC87U-1C70:/jffs#