I'm not sure your theory about the soaking up is correct. But anyway yes, it sounds like you need to remove this non-decomposed material from the planting area and start over. In future do not dig fresh coarse organic matter into soil. Instead apply it to the surface as mulch.

Also if your trees were doing great before you added the bedding apparently your soil didn't need to be augmented. If it ain't broke...

Interesting that pine shavings worked into the soil "a couple of years ago" are not decomposed (according to ^^^^). Why does it ( 30 cubic feet - a few years ago) "need" to be removed now? I'm not commenting on the practicality of this advice.

They should have decomposed in a couple of years unless you are in an extremely dry climate. Where do you live?

What probably happened is that the wood sucked up all the nitrogen from the soil in the process of decomposing. Fresh wood will do that - it is extremely low in N. Plants can turn yellow and even die.

Or, if the bedding was very high in manure it may have had too much soluble N, which can also harm plants.

In any case, after two years the soil is probably fine. Nature rebalances itself. Can you see actual wood shavings in there if you stick in a shovel?

One way to test it is to take some soil, put it in a pot and plant some bean seeds. If they sprout OK and grow, the soil is OK.

Thanks for the replies and advice:)

To Embothrium: In hindsight, the bedding used to soak up the pet urine most likely soaked up the water in the soil, wicking away water from the tree roots. That's my hunch since the trees deteriorated in the same manner as when irrigation is turned off in this desert climate that I live in. And you're right, if it ain't broke... but because the soil in that part of the garden usually runs really dry, I somehow thought the bedding would help retain more moisture. Duh, what was I thinking?!?!?!

To rifis: In the desert where I live, it takes forever for anything to decompose if I don't water it. Hmmm, I wonder what mobster treasures have been found in the desert out here? :) Anyhow I agree with you. Manually removing 30 cubic feet of bedding with or without the soil will be a lot of work but it might be the most effective option (if the seeds don't grow per toxcrusadr's advice). It took me 30 minutes today to sift a gallon's worth of soil with minimal results. No can do but seeing the rate of (non)decomposition of the bedding and the time-consuming task of sifting, I might have to remove the soil and start over as Embothrium suggested.

To toxcrusadr: I live in Henderson, Nevada, an extremely dry desert climate. The bedding contained duckling urine and feces, so I'm guessing it was high in nitrogen. The leaves turned yellow and brown and new growth stopped altogether by next season even after I hand-watered throughout the spring and summer months. I dug through the soil today- dry but bedding is still intact and moist (irrigation has been turned off for a year and last precipitation was 2 weeks ago). I will take your advice and do a test run of the soil with some seeds and will post the results. That's great advice, btw!

I think the bedding had too much nitrogen and killed the plants that way. Poultry bedding in notoriously "hot" and you have to use it in small quantities.

The roots would have gone to the shavings for water - they can's "suck water" away from anything.

In the future, compost the bedding until the wood is broken down, than add it to the garden.

You definitely need a compost bin if you still have those ducks. You can keep it moist with dishwater or whatever.

My mom lives in Albuquerque and has buckets in the kitchen and bath to collect wastewater. It takes a whole bucket worth of water to get hot water out of the shower tap, so there's a bucket full she can pour either in the toilet tank after flushing or take out to water plants. And so on. Even here in MO I've watered trees with bath water in bad drought (the epic 2012 drought got me started on that). Or I throw my dishwater and rinse water over the deck into the yard. Amazing how much water we use in a day.

The best solution to too much nitrogen and undecomposed wood shavings is going to be moisture. But it's likely the nitrogen that burned the plants is gone by now, one way or the other.