Sometimes you may need to factory reset your phone for any reason including a fresh re-install of new stock or custom ROM, or you just want to make a factory reset before selling your phone or returning for warranty. Doing a factory reset in stock recovery ERASES EVERYTHING on your phone. However, doing a factory reset in CWM or TWRP does not, it only erases your settings/apps.
If you have rooted your Samsung Galaxy Note 4, Note 3, Note 2, S6, S5, S4, S3, S2, or any other Samsung devices including tablets, mostly like you have installed a custom recovery like CWM or TWRP. Well, if you want to receive stock OTA updates (perhaps you want to try the latest firmware that came out last night and you are still on stock firmware), you will need to re-install stock recovery.