What should we do when we get duplicate chosen? I.e I have a forsaken Named "Bob" and in this round there is a chosen "Bob" again
Depends on what name you're refering to, if it's their actual civilian name being the same, then its just rng coincidence (as improbable as that is). If it's their codename ie Reaper, Oracle etc, then what happened here is that you got two chosen of the same personality archetype back to back, explanation of how this works mechanically will be below the proposed fix. To hopefully resolve the issue, no fix for the codename currently as of version 40c (outdated I know, but it's my quickest access to chosen atm), you would want to go into their profile and change their portrait directory to differentiate them visually. Explanation about codenames below based on my understanding of them.
The game assigns specific statistical values to a chosens personal values: morality, confidence, etc; and from these values, assigns a specific alias to offhand reflect that chosen as a type of hero/obstacle depending on how you look at it. An example being the Reaper codename denotes that the relevant chosen has high confidence (core) and low morality (minor) while, say, ExampleGoody (I don't know much on the other codenames) would denote high morality (core) and innocence (core) with low dignity (minor). I could expand upon this further by going into linked values between chosen and relationships (and would if requested) but that is heavily off topic to the matter at hand.
tl;dr A chosen's personality values is what determines their codname/alias.
If the same codename situation still bothers you after defeating the Bob2 round, you CAN change the alias after capturing and turning Bob2 into a forsaken. I use it on all my forsaken to give them fitting names in reverence to their corruption... or erase them from your forces like mentioned earlier.