What are the risks of having to be on long term gerd medicines due to chronic condition? can anything be done to minimize risks?

Well tolerated meds: In general, proton pump inhibitors are well tolerated. Occasionally, they may result in headache or altered stool pattern. Rarely, they may contribute to hypomagnesemia (low magnesium blood levels) & increase risk of clostridium difficile infection. Significantly, particularly in postmenopausal women, they can increase risk of hip fractures. Checking a bone density scan can help define this risk.

Many risks: Long term proton pump inhibitors are associated with increased risks in microbial imbalance, nutritional deficits, osteoporosis and depression/anxiety/dementia. They are difficult to stop due to a rebound hyperacidity. Depending on your chronic condiditon there may be better ways to treat it. Diminish risks by taking probiotics, vitamin d3, magnesium, and strontium.