Seems strange, OP. My DS has been on them for six years, at one time on 30 mg a day. My understanding is they have a very long activity time (wrong definition!) so, for example, when DS had to have a pH probe test, he had to be off the Losec for a week so that its effects wouldn't be felt.
(I noticed on the sheet that things like Zantac were much shorter).
Having said that, when he was on 20 or 30 mg a day, we did split it into two doses, but that was more that his tummy seemed to be affected by having too much at once, rather than the reflux.
(My DS has it for classic reflux associated with his wider condition, so obv very different to your DS.)
Also we have always given it at the same time as his milk feeds (he was wholly tube-fed until he was four, still partially tube-fed). His gastro has never said about timing it 30 mins before feeds, although when DS was on domperidone, he was emphatic about it with this.
It sounds like it might be worth phoning the consultant's office and seeing if you can talk to them for clarification. I hope it gets sorted.
(Blimey, am a bit worried now we've been doing it wrong for 6 years! But it has worked - without question.)