Is rooting possible on an already encrypted device My device is already encrypted. It is not rooted.
Note 2 GT-N7100.

I made an attempt to root it earlier a few months back and it tripped the KNOX counter and void the warranty. But it didn't root the device. The SuperSu would crash and it won't allow to apply the update from the play store.

Now I am AGAIN trying to root it and install TWRP recovery, using ODIN 3.9. It just restarts and when I try to boot into the bootloader to check its the same Samsung recovery, no TWRP.

P.S: ODIN shows the "PASS" successfully and has all the indications that the TWRP has been installed.
In short: Yes, you can root an encrypted device, because "encryption" only encrypts /data and not /system. 

Are you sure you are using the correct settings in ODIN for your device and following all directions completely on whichever tutorial you are following? Please cross-reference your tutorial with the XDA Guide (highly recommended that you follow this guide; I can post the instructions here for permanent refernce upon request).