@Twinkle - with NSSU (default settings) what should happen is that the BK RE gets code upgrade 1st, and is then re-booted. LC is next, and Master RE last. When Master RE re-boots, the former BK RE will now become Master. Now for NSSU you must also turn off things like GRES and NSB (you need to do this before you start the NSSU process) so when when switch-over from former BK to become new Master there will be a HIT! Former BK RE needs to perform some re-learning/etc. Exact time for hit depends on network but I would suspect 30 seconds to a few minutes might be normal.
You will probably want to have you server admins check their applications after the upgrade to make sure none are down or stuck due to network interuption. I believe things like EPIC/etc. maybe affected. If you remote WLAN AP switches are split or dual connected to different core EX4600s, then there should be no interruption for these.
Remember to turn back-on GRES/NSB after the upgrade, and then if you wish to switch back Master ownership of RE, you should be able to do this without any hit. Since these are core switches, I assume you also have some form of NSR enabled.
I would also assume you are upgrading to 14.1X53-D40. I would NOT recommend considering a move to 16.2 for this platform. Next move forward after 14.1X53 for EX4600/QFX5100 would be something in 17.x train.
Hope this helps.