They are checked by default, so perhaps as you suggest an update may reset it.

Are you running avast as a limited user ?
That may be something else which could restore any changed settings.

Though my question is why wouldn’t you want avast to do some housekeeping. It may well be a better option to increase the number of days that the data is retained.

I have my “Delete scan logs older than” set to 30 days and “Delete temporary scan logs older than” set to just 1 day. I can’t recall what the defaults are but you could set them to 60 days and 7 days respectively and see if that sticks.