Questions are posted in the main C&C forum, not these subfora. I've notified the moderators to move it.
To your question, it depends on what gets changed. Generally, yes, the civilopedia will automatically update for most mods. New buildings, units, techs, resources, promotions, policies, etc. will be automatically included in the Civilopedia. Most mods only deal with these types of things, so you're fine.
Now, there ARE a few things that won't be included. Entirely new types of content (like the deities in my Mythology mod) will not be shown at all. The "concept" page of the Civilopedia has to be updated by hand, and doesn't support the addition of any new concept groups unless you make significant changes to its code. Adding new Eras to the game updates the Civilopedia in most areas, but not all.
In fact, the problem is usually in the other direction, where the Civilopedia is showing a bunch of things that you'd prefer it not to. This is especially common with "hidden" buildings and policies, where you're using these things in Lua to modify some other system that has no XML equivalent. For instance, in two of my mods I have specialists designed to add Happiness. (Priest in the Mythology mod, Empath in the Alpha Centauri mod.) Since specialists can't actually add Happiness directly, I instead use a Lua function to add instances of a repeatable +1 Happiness building as necessary. So someone going into the Civilopedia will see a listing for that building, despite the fact that you can't built it.
Or, similarly, my Mythology mod has 21 4-building chains, where none of the buildings are buildable. Based on which gods you follow, you'll start with the level 1 building in a handful of chains, and the buildings will automatically upgrade themselves to higher levels as the game goes on. While it's nice to be able to go into the Civilopedia to see what these things do, the default UI puts all 84 of these in the Ancient Era's box.
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