I have flag iris in my pond and want to know whether I cut down the main flowering stem or just pull off the dead flowers and leave everything else intact?
I deadhead the flowers as they fade. Then when all the flowers on the stem have been spent you can cut the stem from the plant.
Here is a link about growing Flag Iris.
Are flags dying when they have tall shoots growing out of them?
Can you be more specific or upload an image of your Iris?
I planted yellow and blue wild Flag iris around my pond. I have a lot of yellow this year but no blue. Is it possible that, like a hydrangea, the flag iris can change color due to the soil conditions?
I don't think that is the case here. Irises can fade over time but they will always have a general hue of their original color. I've attached a link with more info on irises.
Exactly what do I do to divide them/thin them out?
Here is an article that will help you that discusses how to divide irises:
I am growing Pseudatas, a pseudacorus/Japanese Iris hybrid. Does this yellow flag iris require a freeze?
Yes, the do require a freeze.
Can you remove the pods on the plants after flowering to start iris in another location?
Yes, Yellow Flag Iris can be grown from seed. Collect the pods produced after the flowers wilt. The seeds must be exposed to cold temperatures before germinating, known as cold stratification. Place them in damp paper towels, roll up in a plastic bag, and store in the fridge for 3 months or until they germinate. When ready, plant in a pot, then in spring transplant outdoors.
Be aware that this plant spreads aggressively. Here is more about this plant:
it would be very helpful to have a picture of blue flag and siberian iris to compare because the description does not give enough information to clarify the difference because the flag iris also has a sword looking leaf
Here you go: