There was a lot of issues switching over from LSD to ULSD in terms of deposits build on EGR components, which may / could have also come from the rampant use of sub-standard biodiesel which is widespread (even today) and home brews.
Around mid 2000s with diesel prices exploding, many people were running home brew biodiesels that is nothing more than filtered used french fry oil and expecting their vehicles to work.... with finely tuned emissions systems, DOCs, and EGR.
One immediate problem that have been hinted at (but haven't seen much published) is when fuel went from LSD to ULSD or to biodiesel (of any % blend above say, 2%), what effect does it have in leaching stuff that is in the system, including corrosion products, varnish, etc.?
What about damage to seals that were not designed for it?
As it turned out, engines that were in the installed base from mid-2000s onward to 2010 had a lot of issues, including EGR clogging with particulates, that seem to have completely gone away recently once the system had a cleaning / replacement of bad EGR components within the past year.