As lillies die back in the fall can you cut them back following the green down the stock or do you need to wait till the while stock dies back and cut all at once?

It's best if you wait until the stem and all turn brown. Then cut about 5 to 10 cm above ground, leaving a short stub in place until next spring. This natural process assures your bulb is mature will be well prepared for winter as well as full development toward putting on an even better show of more flowers next year.

You can, however, cut as soon as the leaves turn yellow and fall off, but understand that the bulb is not yet fully mature or hardened up for winter and early spring wet conditions (which lowers it's resistance to things like bulb rot).

I would wait until the entire stem is brown, too, or at least the entire stem begins to turn brown (after being yellow).

The normal process of lily die back dictates that essentially the entire stalk should turn color at the same time. If your lilies don't do that, it doesn't necessarily mean something is drastically wrong, but there must be one or more reasons why. Perhaps an insect infestation on part of the stem, or mechanical damage, disease, environmental stress, etc.

Remember multiple cuts mean multiple wounds that are vulnerable to infections if you are cutting down to live or dying material. This would include virus transmission via your pruners if you cut one virused lily and then another lily.

Ok thank you very much.