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My friend says you can, I was wandering if you really can.

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If you caught Deoxys in Space after shattering the meteor, you cannot fight him again.

If you beat Deoxys in Space after shattering the meteor, you can fight him again at Sky Pillar, after beating the Elite Four again.

If you caught Deoxys in Sky Pillar after beating him once, you cannot fight him again.

If you beat Deoxys in Sky Pillar after defeating him once, you can fight him again after beating the Elite Four again.

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that means yes, you can re-encounter him
Idk why this has gotten downvotes.

TL;DR you can encounter Deoxys again if you beat the E4 and go back to Sky Pillar.
what's with the downvotes?
Idek tbh, lol