First issue Underlining text with 'underbar' in the master document (e.g. _Siti)_ enters an endless loop when trying to compile to PDF with the fatal effects described above. Funny enough it compiled (sometimes?) before in a child document but did not when included in the master. And: I can stop the destruction of files only if I cut the power off immediately after the loop started!
I see what you mean, and I can reproduce it. I haven't observed any files being deleted though. It will take some time to check all this, please be patient. There are many packages included with classic thesis template and one has to go removing them one by one until everything works again.
Second issue Using Jürgen's nice and useful new modules like csquotes (context-sensitive quotes) fail to work in classicthesis-LyX-v4.1, i. e. are not available in full in the Insert > Custom Insets menu and produce quite a number of errors
I unfortunately cannot even test this as I don't see the module in my modules list. But again, clashes are possible, not all (versions of) packages work well with one another.
Now there is hope these problems may have been already resolved in the a bug-fix version of the v4.1 template in the 4.2 bundle which you told me. I will download the 4.2 version and then see to it.
I don't think the above issues were addressed in 4.2. I'd rather try to remove (or comment out) calls to packages in classicthesis-config.tex and see if that helps. You can have the command "top" running in a terminal window. Once pdflatex enters the loop (CPU usage 100%), just kill it with a 'k'
