en and y can usually gramatically be swaped, but they are semantically different.

In contexts where they both mean a change of place, en implies that you’re coming from whatever place is mentioned while y implies it to be your destination.

Example :

• J’y viens means I’m coming to it.
• J’en viens means I’m coming from it.

In your example, Il represants the assertion from your previous sentence. Since the purpose of your second sentence is to justify that assertion, your reputation is the justification, from which comes that assertion. that from relation is already marked by the preposition de, while what you are actually describing with the verb va is the movement from your repoutation to the conclusion in your previous sentence.

In short, Il y va de ma réputation de ma réputation que je ne pourrai pas toujours être là.

But I guess the en form imposed itself from its existence in other contexts – il en va de même – and a lack of familiarity with the correct form due to its relative rarity.