The new USFWS decon (cleaning and disinfecting) protocols were finally released last week: http://whitenosesyndrome.org/sites/default/files/resource/national_wns_decontamination_protocol_v_03.15.2012.pdf
Regarding your questions, I am not aware that any testing has compared the various disinfecting methods for degradation of gear. The only testing for degradation of the chemical versions was done by Dr. Hazel Barton on Sterling ropes a couple years ago: http://www.caves.org/WNS/Sterling%20Results.pdf
That said, common sense would tell me that using the 122F water method for the disinfecting portion of the process would expose the gear to less chemicals, the person doing the process to less chemicals, and the environment to less chemicals. That would be a no-brainer.
However, in speaking with Aaron Bird, Chair of the NSS Safety and Techniques Section, who prepared the various NSS videos on proper decon techniques, including how to protect oneself while doing them, he raised concerns about the safety of massive hot water for a decon station at a caving event. I can envision a giant witch's cauldron at a bonfire - etc. You get the picture.
The point is that location, conditions, availability of materials, and volume may lead to different decisions on methodology at different times.
Regarding the cavers you see in Indiana not cleaning their gear, that's both a scientific and a political discussion.
From a scientific perspective, decon is one of several management tools along a spectrum of risk management intended to slow the spread of WNS by preventing or lowering the potential for humans to inadvertently transfer spores. Biologists don't believe they can stop bats from transferring WNS, so the one they can advocate for is reducing any human vector potential.
At the top of the risk management list is the recommendation to never use any gear that has been used in a WNS-infected area in any unaffected area. No matter how much you believe or don't believe humans may transfer WNS, if you don't take anything out of the affected regions, you won't move anything. Pretty absolute.
Next would be decon. While the decon techniques, if done properly, will kill the fungus, there is plenty of room for human variation in how well the process is done. The ability to go back to your research lab, under controlled conditions, or your home or a caving event decon station, is very different than out in the field. In Indiana, where many caves are nearby, the ability to do it is quite different than out in the vast West, where caves may be a day or two hike or horseback ride out in the Wilderness, and water in short supply.
This is one reason why the protocols are the way they are - to provide alternatives, yet make them as practicable as possible. Hey, they are a pain - cavers and researchers agree - they take time, curtail the number of caves one can visit or study, and have inherent risks.
Next on the list of risk management would be simply cleaning your gear. Cleaning your gear of all organic material - mud, particularly - will remove most of any spores you may pick up. It won't kill any that are left, but you've reduced the number, and thus the probability of infection. Scientifically, we still do not know the number of spores required for infection, the critical mass known as the Multiplicity of Infection (MOI), but less is better.
Further, as a caver, I cringe when I see people pull out gear or clothing caked with mud from previous trips. We should all be cleaning. It's safer - you get to examine your gear for wear and tear - and it is more respectful of the unique environment that each cave has, by not inadvertently moving microbiology from one environment to another where it may not have previously existed. It's simply good caving and conservation practice.
"Is there any logic behind deconing your gear after visiting a cave with G. destructans if you're going caving in another cave with it also. " A great question. Personally, I don't believe so. I also personally don't believe that a caver or researcher in California, for example, going into only California caves, should be deconning. There's no WNS there, so that caver or researcher can't possibly move WNS. And yet, on U.S. Forest Service land nationwide, and some other federally managed units (some National Park caves, some BLM caves), it is required.
Wildlife managers are aware that fewer people are deconning, and are concerned. Add to that the fact that many cave visitors are not NSS-affiliated cavers and don't know about decon, or even WNS. This is something we've been telling USFWS since the beginning. There is some agreement among wildlife managers in the East - particularly in the WNS-saturated areas - that it is pointless. By the way, I would not consider Indiana to be saturated - yet - and would consider it appropriate both scientifically and politically to decon there.
Politically, decon does show the public that agencies are trying to do something. Cave closures are in this category as well, but that's a whole other topic. However, top epidemiological scientists believe that to contain infectious diseases, one assumes they can be moved in a variety of ways, and on a variety of objects. Hence last fall's Bulletin from the U.S. Geological Survey urging universal precautions.
Again, politically, as long as the top agencies are urging this for the public, the media and other publics believe it. Thus, anyone not doing it is perceived not to be helping. Politics being perception, that perception is part of the contextual reality in which we, as cavers, must operate. Put bluntly, if the Indiana state and Hoosier National Forest biologists continue to see cavers ignoring decon protocols, how much more likely do you think they will feel toward reopening the caves they are responsible for? Further, while everyone knows bats are spreading WNS, having people ignore the protocols on private lands clouds the issues and makes arguments against possible human spread more difficult.
That said, I have participated in a subcommittee of the Northeast Bat Working Group which has recommended that USFWS change how the decon protocols are used in different regions. Working with state wildlife officials from NY, PA, and West Virginia, and USFWS reps, we proposed lifting the decon requirements in saturated areas, for the reason you cite, among others. The rationale is that by demonstrating through policy that these sorts of restrictions are truly temporary, cavers and other cave visitors elsewhere - at the WNS front lines and in unaffected areas - would be more likely to comply with temporary restrictions. This will be the subject of a session at the upcoming National WNS Symposium, June 4-7, in Madison, Wisconsin.
Further, I do urge all cavers to think beyond their local haunts. The response to WNS is national, and we need to not think parochially about our caving. What goes on in Indiana doesn't stay in Indiana, in this viral Internet age. Wildlife officials nationally have weekly conference calls, so they all know what's going on.
Cavers are working diligently in other parts of the country to re-open caves. Meetings are actively taking place with federal land managers in a number of areas, trying to balance bat conservation with other conservation and recreation concerns. Frankly, they need us, and we need them. They don't have the resources to inventory their caves and bats - we do. We don't have access - they do. This is a no-brainer. Decon, politically and biologically, will be a part of that equation, certainly on federal and state lands.
Now, a word about the decon protocols themselves: a few years ago, we pushed hard to get Dr. Hazel Barton involved, and she has been - doing an absolutely yeowoman's job educating primarily mammologists about microciology, the cave environment, and frankly, caving. There are other NSS member scientists involved in the protocol development, such as Judson (Jut) Wynne. Their focus, however, is on what is effective in terms of decon materials and methods - the science, not the politics.
The politics of decon are that these scientific recommendations then need to be applied in the real world. That real world includes the political dynamics of cave closures, relationships between cavers and federal and state agencies, political pressures brought by outside entities, such as the Center for Biological Diversity, and, yes, personalities.
The NSS has had Memoranda of Understanding with all the relevant federal agencies for many years, and has been methodically updating them of late. Within those national MOUs, there are a myriad of local and regional MOU's where grottos, cave conservancies, regions, and surveys have access to caves, manage caves, survey caves, and do a host of projects that are beyond the resources of the agencies. Some of the discussions about re-opening caves are taking place in the context of these MOUs, including creating new ones to solve some of the local or regional issues. From what I've seen, decon is a given. Decon is a given by referencing the current USFWS protocols. As those protocols evolve and change, that reference will not have to. Further, the new USFWS protocols permit agencies to have their own supplements, which can provide for things like not having to decon between caves close together, or making practical changes for back country challenges, and more. I truly believe we will make more substantive progress on both the scientific and political fronts on decon and its application by working through the protocol process, not outside it.
So, I would urge all to clean gear as good caving practice, and to think more broadly, not parochially. We're all in this together.
(edited to correct typos)