On ne force pas son destin, on ne peut en modifier le cours à sa convenance.
En in this sentence refers to destin. You could rephrase this part as:
on ne peut pas modifier le cours de son destin à sa convenance.
What is happening with Google Translate is not for me to say but I can tell you by experience that it is not the best tool you could use and there are better online translators.
Here's what DeepL returns:
one does not force one's destiny, one cannot change its course to one's liking.
Which to my mind is a much better translation, en which in the French sentence relates cours to destin, being rendered by the possessive adjective "its" which links "course" to "destiny".
Although this is probably not the most frequent use of en as a pronoun we can still encounter it to express "of it/its" "of them/theirs" etc. In French as well in every day speech a possessive adjective would be used instead.
- Ces roses sont magnifiques, j'en aime beaucoup l'odeur.
- Ces roses sont magnifiques, j'aime leur odeur.
1 & 2 mean the same thing, 1 sounds more literary.