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If you have an IC join a unit does it lose its faction or does the entire thing count as both factions?

Same for something that is made of multiple unit types. Does it count as all unit types in the unit or not?

Mainly asking because of abilities like preferred enemy, or things that only affect models from a particular type or faction.

If an IC joins a unit, it is considered to be part of that unit for all rules purposes.

This means that if, for example, a Space Marine Captain joins an AM blob squad, models with Preferred Enemy (Space Marines) will not benefit, but models with Preferred Enemy (Astra Militarum) would.

With abilities that affect models from a specific faction, the wording is usually "Models chosen from this Codex" or something similar, so while thee Captain (in the example) is part of an AM unit, it is still a model chosen from Codex: Space Marines.

What about if something is a unit type difference. Such as a unit made of calvary and beasts and you have preferred enemy beast?

In that case it is unknown how it works.

If a cavalry IC joined the unit of beasts, it would still be a beasts unit. If it was a mix (similar to what Tau can pull off), it's a bit different.

Unit Types are Model specific, it is irrelevant which Unit the Model is in as to what Unit Type it has.

So if I have preferred enemy beasts and I assault a unit of beasts and calvary would I get the benefits or not I guess is what I am asking.

All I can do is throw up my hands and grumble, then House Rule it in some fashion to make it work.
This is because what you are describing is a known issue within the Rules themselves, a Black Hole which has no way to resolve and interpretations which are based solely on our attempts to side-step the issue entirely. The simple reality is that we have something occurring on the "Unit Level," a Shooting attack, that is reliant on something found on individual Models, the Unit Type. We need something informing us how to proceed, either to tell us that the entire Unit is a suitable target or to provide us with instructions that will detail just how we go about resolving this Special Rule against a 'Mixed Unit.'

Take it one further:
There is a Model which has Preferred Enemy (Independent Characters) and how do we ever resolve that one?!

I have been playing it as made up of all the unit types inside, but I dont know a fair way to do it since my wolves are build around preferred enemy use.

It is going to need a House Rule in any case....
Maybe something half way between all or none; the Preferred Enemy Rule triggers if more then half the Unit meets the conditions?

So what would happen if two independent characters from separate factions joined as one unit? Lessay a Dark Eldar and Eldar IC. How would hatred, preferred enemy, etc apply to them?

Work out who joined who. SImple.

Nosferatu1001:
Two Independent Characters join a Third
That original Independent Character then moves out of coherency
The other two are still in coherency with each other

Which Unit do they belong to?

I just contacted nova and they are running it as a unit is made up of everything inside. I think that is how BAO and thus most major tournaments are going to be running it.