I read this a lot, but I don't remember ever having such problems...

I almost always used WinHTTrack rather than the command-line version, and
there I've left for ages "Do not purge old files" to checked (under Build); I
have done almost all my updates with that checked, and the few times when it
looked like old useless files were really starting to take up too much space,
I always made a copy of the project before launching the update with "purge"
enabled...
And even then, I unchecked that box with a lot of dread!
I think I actually even put back then the smaller files, because I actually
like to collect old stuff and look at it every now and then :)

I'm really a little baffled to find out that the software's default is to
purge, the disadvantages of the other option (taking up a little space) are
way less problematic and *fixable* then files' deletion!!!


So in any case, it looks like enabling that option prevents at least the large
majority of these problems, so do set it always enabled, and always pass -X0
to HTTrack (damn, the command-line version doesn't even support configuration
files!)!