What I did to install the system update and then re-root.
- First, I restored my stock backup using TWRP.
- Reflash the stock recovery from firmware.zip from OTA_K2_CL_JB422_SENSE50_MR_Sprint_WWE_Boost_3.05.653.4-3.05.653.3_release_389326.zip with fastboot. fastboot flash recovery recovery.img
- Rebooted my phone and simply checked for update and let it install.
- After that, I did a factory reset to make sure I have a clean update (optional).
- And finally I used fastboot to reflash TWRP. Now, I'm good to go with the latest software update. Thanks for the help.