There's an issue with handling responses from plugin. When postprocess changes file to be smaller than original - HTTrack accepts pointer to new file sting, but ignores new length. This causes garbage at end of files and occasional crash (processed file has same length as unprocessed file).
It looks like this bug was introduced in version 3.48.12 (3.48.11 works as expected).
I can provide my plugin if it'll help, but it's integrated with python, so building it will require additional dependencies.