PPI's do reduce absorption apparently. My friend is getting iron infusions after a long time on omeprazole. There is no other reason for her low iron.

I am really mystified as to why doctors continue PPI's when they were intended for short term use.

The body adjusts, I have read, by making more acid so when you try to get off a PPI, you actually feel worse than when you started. I got off by transitioning very slowly (one day of a week at a time) to Pepcid and then slowly cutting the Pepcid. It took months.