Learn French: Il est absent, en effet il est malade.

This sentence shows the opposite relationship to help you tell them apart! Words like alors (so) and donc (therefore) introduce a consequence. Here, en effet (indeed / in fact) introduces the cause or explanation. If we wanted to use a consequence word, we would have to flip the sentence around: Il est malade, donc il est absent (He is ill, therefore he is absent).

Can I translate en effet simply as "because"?

In terms of meaning, yes! It provides the reason for his absence. However, structurally, en effet usually acts as a bridge to confirm and explain what was just said in the previous phrase. If you use "because" (parce que), you don't need that pause: Il est absent parce qu'il est malade.

Are en effet and en fait the same thing?

They look similar but are used very differently! En effet is used to confirm or explain what was just said (like saying "Indeed, this is true because..."). En fait is used to contradict or correct something (like saying "Actually..." or "In reality..."). Since his illness confirms why he is absent, we must use en effet.

Why do we repeat il est in the second part instead of just saying en effet malade?