Greetings!
I'll start by saying I have no clue what caused it, nor how to recreate it.
I've swapped over to water gateways instead ^^
Was originally using particle portals, but noticed after some time the particles vanished, while the gateway still worked.
Changing the types until it was particles again temporarily fixed the issue, but it'd return after some time.
On a side note, have you considered making End Gateway gateways? ^^
Fancy looking interdimensional gates