Great points, Michael. I suspect we are attempting to accomplish the same things with slight variations. And i appreciate your reasoned response. As we are dealing with trees in pots i too believe it is often environmental issues as opposed to pathogenic. Pot size and type has a great affect on the situation. I find this very important in the recovery of my collected Yamadori. Yamadori are almost always in sub-prime condition before collecting and removing them weakens them more so. I collect primarily conifers, Shore Pine, Hemlock, Sub Alpine Fir, Alaskan Yellow Cedar. My success rate has increased markedly with bare rooting and removing all dead and decaying root matter, and all compacted soil. I take care to add back a small percentage of site soil and surrounding litter to the pumice. For beneficial fungi purposes. As well i use sealant on any root cut over 1/4 inch. The grow boxes are built to hold the remaining roots plus 1 inch around the outside and 3 inches below the root mass. Depending on the species, extra space may be allowed above the root mass. For example: Hemlock are very dependant on the top mass of fine feeder roots.
In the winter of 2013 i had a group of expensive JBP that were purchased late fall 2012 and set out in the nursery till spring. They were in 8 gallon nursery pots and compacted roots, mostly field soil that had been transferred to the nursery pots two years previously. Life created personal distractions for the winter and early spring, and we had a very wet winter. All of the JBP started to deteriorate very quickly by the time i noticed their condition. I checked the first one and found a mass of rotted roots. Smelled bad and the roots were sopping wet. Subsequently i consulted with my teacher who advised bare rooting using the process i use with collected trees. I did all the same way and they all bounced back within two years. They are now in Anderson flats and being developed and undergoing early stages of ramification. For aftercare i used sphagnum moss on the surface to prevent drying out and placed in full sun but out of the wind. I also washed the foliage daily which conifers are used to in this rain forest climate.
Steps taken during the repotting process also affect the outcome, misting the tree, roots, careful handling of the healthy roots, gently picking out, rinsing out the compacted soil etc. With proper training and practise, bare rooting is a very useful Bonsai practise for difficult cases.