I ve been using omeprazole for last 3 yrs & had some side effects, if I stop, silent reflux returns + sore throat n cough, any alternative treatments?

Other choices. There are several other choices when it comes to treatment of acid reflux. You could try another medication like Omeprazole such as nexium, prevacid, protonix, or aciphex (rabeprazole). You could also try a different type of medication such as zantac or pepcid.
Try Zantac (ranitidine) or Pepcid. Omeprazole belongs to a family called ppi. You may want to try a different type of acid blockers: h2 blockers, such as zantac (ranitidine) 150 mg twice a day, or Pepcid 20 mg twice a day. Both are orc.