Flap surgery is advised to clean the areas of gum, which cannot be reached by normal scalers.
Most of the times, full mouth flaps can be avoided by thorough deep scaling (sometimes under local anesthesia).
After two or more sittings of deep subgingival (below the gums) and topical (or oral) antibiotics, case can be reevaluated. Only those areas of infection that persist even after this should be planned for flap surgery.
Next Steps
Take multiple opinions: experienced general dentist, periodontist, etc.
Health Tips
Don't jump into full mouth flap surgery. Also, ask your orthodontist to check for root parallelism of teeth.