Background
DexNav chaining means the number of hidden pokemons encountered and defeated/caught consecutively.
The chance of encountering shiny pokemons or pokemons with high number (>3) of IVs that equal 31 increases. The latter is also coincided with higher level (+10), possessing egg moves, and less commonly so hidden ability.
It is known that the chain will not break if the type of hidden pokemon encountered differs from the previous one in the middle of a chain. One can be assured of this by noting: 1) the level increase due to chaining (+1 per 5 chaining) is not broken; 2) encounter of shinies shortly after such switches.
Question
Is the chain unique to a specific pokemon?
For example, suppose I am chaining on Ditto on the Mirage Island. I have defeated/caught 100 Dittos. Now I go on to defeat/catch 30 Munnas. When I come back to chain on Dittos, is the probability of encountering a shiny (as well as high number of perfect IVs and so on) equal to having a purely Ditto chain of 131 or 101?
How can we ever know?
For example, it can be considered as confirmed "no" if I encounter a shinny Munna from one of the 30 hidden Munnas in the above scenario. Since the probability of encountering a shinny Munna within a chain of 30 is near zero, the chain likely was continued from the 100 ditto encounters.
Best Answer
No, I'm pretty sure that the chain is the same for each Pokemon you encounter, as long as you don't break it.
If a Pokemon appears in the overworld that is different from the one you were chaining before, you still have to faint or capture it to continue your chain. This means that every hidden Pokemon affects your current chain. The chain is tied to the DexNav, not to the Pokemon.
And remember that the rising levels of Pokemon in your chain reset after 100 encounters.