Yes I think there are new fears about these medications.
Another one is that they may interfere with the microbiome (those bacteria that live in your gut) and that can cause all sorts of problems. I used to use omeprazole (and at times lansoprazole myself).
One of the things I found was an almost tolerance like effect from taking them regularly where after a few weeks they seemed to just stop working.
Not sure if anything is conclusively proven though - is your doctor a GP or a gastroenterologist? If you are really having problems might be worth going back to her and explaining this.
The risks may be worth taking if it is really affecting your quality of life. You might also benefit from a specialist opinion if you aren't seeing one already.
Same thing with me. They seemed to lose their effectiveness after a week. I had to start and stop. I will seek the advise of a Specialist. I used Lansoprazole in the end as I felt they had less side effects. I take the odd Zantac from time to time. Maybe a physical fix would be needed but it would be the last thing i do.
Long term it may be safer though.