Yes, you are right.
By default, each week job will be placing downloaded files in the same folder on your disk and the MHT file will be overwritten.
To prevent this, you can special macros, [%d] and [%t], in "Save in Directory" parameter ("Project Settings / General" dialog).
The [%d] macro inserts the current day it the directory name, when the [%t] macro inserts the current time.
When using these macros, each week the new download will be saved in a separate folder (based on download date, time) and the MHT file should be overwritten (because it will be saved in different folders).