Let’s say I’m chaining zigzagoon and I scare away a poocheyana that was found instead with the Dex Nav, will the chain break?
If you have any encounter other than the Pokémon you are chaining, your chain is broken. This includes wild encounters, DexNav Pokémon other than the one you are chaining, scaring away an DexNav Encounter, etc. Essentially, anything that isn't your Pokémon. Also, you always have to faint of catch the Pokémon you are chaining, you can't run away. So, yes, your chain will break.
Source: https://www.serebii.net/omegarubyalphasapphire/dexnav.shtml#:~:text=DexNav - Chaining A lesser known feature of,and you are almost guaranteed to find one.
Hope I helped!