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The Black Templar codex can be annoying to read, but even with FAQs I still have problems with THESE damn flags:

Fighting Company Banner
Chapter Banner
Sacred Standard

OK, lets start, sorry for posting points but I need to say them

A Command Squad (non-terminator) can take a specialist, (Fighting Company Standard Bearer)
Now if I want one of the other flags I need a Sergeant with Terminator Honours, then it can give a terminator Honour to the Fighting Company Standard (so it can take wargear)

But let's say I want a Chapter Banner instead of the default Fighting Company Standard...
... am I paying a total of 50 points for it (standard bearer price + chapter bearer) for this?

I know you can only have one flag, and what you purchase replaces the Fighting Company Banner.
A Chapter Banner is pretty much an improvement on the default Fighting Company Banner (despite ignoring rerolls for pinning tests), so that double price is understandable.

But here's the problem, if I wanted a Sacred Standard is be 45 points (standard bearer price + sacred standard) which is overpriced compared to Chapter Banner.

I'm very confused how the selecting/price for all 3 flags work. Can someone clear this up for me?

you've got it right, there's no rule that lets you take wargear away from him, so you just have to pay for the new flags on top of the points you are paying to make him a terminator honours standard bearer, and then you lose the effects of the Fighting Company Standard by doing so.

You appear to have it correct.

I knew Black Templars could be expensive, but really?
Picking the Sacred seems stupid compared to the chapter...
... but it's quite a high price to do so

Black Templars suffers a bit from being a rather old codex. If/when they recieve a 6th edition version; i'd say you can safely expect a cost reduction for most things, and/or a couple additional effects added instead.