I received a black pine bonsai from a family member a couple of years ago. I live in the high desert in CA, and it was fine till this winter. I cover it at night when there is a big frost, or if it snows, but something happened and now the needles are turning brown. It started at the tips and now there is just about 2-2.5 inches of green near the base of the needles. the rest is brown. when it's cold (below 60) I watered it every other day and sometimes every three days. During the warm months I water everyday. It is in a ceramic pot with two drain holes in the bottom and it has a humidity tray. It gets morning sun, and is in the shade during the hottest part of the day. Did I kill it? HELP.

JBP in the desert! You did not shoose the best species to start with. It is a temperate species, if you are not in a temperate climate JBP may be quite a challenge. If it is dead or alive is impossible to tell without a photo.

Do you have some pictures?

It is a bit hard to diagnose from a distance. I am not convinced that the location where you are is a problem for the tree if indeed protected against full summer in the hottest months. In fact, [japanese] Black pine thrive in drier, warmer climates than mine. It feels like you have the right climate there.

It is a bit hard for me to relate, as my climate is so much milder! I need to be careful watering black pines because it is so humid here, in comparison to where you are, and I need to hold back on giving any care tips because our challenges are so different.

Pinus thunbergii is listed as hardy in usda zone 5-8. I am not sure If there are any american deserts that low in USA. I woud guess OP is in zone 10. It does not mean that it is impossible to grow them, just that it is harder than for LB and me, we are both in Europe similar to zone 7 but a lot wetter espessially in winter. Indeed none of us can make any targeted advice on such a different climate. Best is to look for bonsai growers in your area and look what species they grow and how they do it.

Hardiness is about the coldest winter gets. It does not say anything about how hot it can get.

Not, California is 7a => 11a.

I know what hardiness zones are my friend. The classification of a place into a zone is based on awerage low in winter, yes that is right. What you are missing is that the zone classification of a tree is based on experience. Some trees have a wide span and some have a narrow span. Growing a tree outside its zone is always a challenge, no matter If it is too low or too high. If it wasen't there would be no need for an upper limit.