In listening to:
Il s'en est allé. Il s'est en allé
the T in est allé is spoken "eh-tallé'
but in s'est en allé it wasn't said.
You could make the liaison in the second sentence between the s'est and the en ( sounds like sétan) but it's probably one liaison too far as you have to make the following one between en and allé ( nallé).
Liaisons if not compulsory are often instinctive and optional and will often depends on many cultural factors and habits.
Hope this helps!
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