> when copying out a file tree HTTrack x64 seems to
> lose a character at the end of each directory, 

What is the exact full path of the files ?
Normally httrackattempt to keep the original filename... unless the resulting
destination directory path is larger than 260 characters (a hard limit on
Windows, also enforced on Linux by httrack)

In such case, directories and filenames are "cut" a little bit to fit the
filesystem limits.