How to edit hidden settings from Developer options?

I'm uncertain on bringing those lost options in GUI back other than to recommend clearing data of Settings app from Settings → Apps → All apps → Settings → Clear data. Reboot and see what happens. In the event of failure, you can consider factory-reset.

That said, if you're simply concerned with changing Window/Transition animation scale and/or Animator duration scale, then you can use settings or content tool which do not require root access. You can refer to Christopher Galpin's method for an approach requiring root access.

_{(Solution tested on Android 4.2.1, 4.4.2, 5.0.2 and 5.1.1.)}

Setup adb in PC and execute

adb shell settings get system  window_animation_scale
 # for Window animation scale. Some ROMs have this key under global table instead of system. So replace system if command gives null

adb shell content query --uri content://settings/system --where 'name="window_animation_scale"'  # an alternative to above command. Make replacements as appropriate

If the first and the second command returns you a decimal and a string beginning with Row:, then you're on the right track. Now do

adb shell settings put system  window_animation_scale VALUE
# Replace VALUE with a decimal, such as 0.75 or 2.0. The minimum and maximum I've seen are 0.0 and 10.0

adb shell content update --uri content://settings/system --bind value:s:VALUE --where 'name="window_animation_scale"'  # an alternative to above command. Make replacements as appropriate

In order to change Transition animation scale, replace window_animation_scale with transition_animation_scale. For Animator duration scale, replace with animator_duration_scale.