This is one of the entries from the Longman Dictionary for the noun "course"
5 DEVELOPMENT [singular] the usual or natural way that something changes, develops, or is done.
It seemed incorrect to me. Shouldn't it be "the usual or natural way in which something changes..."
The only definition I could find for "that" that could fit here is:
that
a. In, on, by, or with which: each summer that the concerts are performed.(source:American Heritage® Dictionary of the English Language)
With this, I could transform the sentence into "the usual or natural way with which something changes, develops, or is done" but I don't know if it is the correct usage.