We understand that long term use of Omeprazole, Lansoprazole, etc, can lead to weaker bones - one internet directory says: Proton pump inhibitors may increase your risk for bone fractures, especially with longer use, higher doses, and in older adults. Talk with your doctor or pharmacist about ways to prevent bone loss/fracture, such as by taking calcium (such as calcium citrate) and vitamin D supplements.
However, we have also heard (from an oncology dietician) that calcium based tablets "interfere" with the likes of Omeprazole.
I think this is going to be half an answer, because all medications have side effects of some sort, and they are probably all dependent upon the effect on an individual.
If you need to take PPIs because of the major condition of having to reduce stomach acid, then you have to keep taking the medication, or an equivalent. You will suffer worse if you don't!
PPIs do, apparently, have a long term effect at reducing calcium, and this may well have an effect eventually, on bone density. So you can have a bone density scan to check, and then monitor it periodically if you are concerned. It is a long term issue.
My very non-medical guess is that if the medication to prevent bone density loss prevented PPis from working, you would notice the effect through reflux.
But you should take this with a pinch of salt until we manage to find somebody qualified to give an answer!
The more of your stomach that you have had removed, the more likely it is that you will find it difficult to maintain vitamin B12 / iron levels, and this can lead to anaemia / lethargy.
Anybody who has had an oesophagectomy or gastrectomy is liable to find that their system does not absorb medication and nutrition in the same way as it did before, because the food does not stay in the system for as long. So it is worth checking. You can have your levels of vitamins and minerals checked.
I have asked a specialist Upper GI dietician - she had not heard of calcium based tablets interfering with PPIs, and could not see why they should if they were taken at different times in the day, e.g. PPI morning and evening and calcium/vit D at lunchtime.
She had done some research which did not find significantly different calcium or vitamin D blood levels in a group of patients who were on PPIs, but the research did not include a bone scan. [It might be that this effect of PPIs only becomes apparent as a long term issue].
Her speculation was that people could try stopping the PPI if they are concerned, or reducing it. If they remain reflux-free then great.
A vitamin D supplement was worthwhile in her opinion, depending on each patient's situation.
Hypochlorhydria, low stomach acid, produced by PPIs, means essential minerals may not be dissolved out of food sufficiently so you may be low on calcium, reducing bone density, iron, causing anaemia, magnesium, zinc etc.
Those on long term, high dose PPIs may well have to take supplementary minerals and vitamins to help absorb them.
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