Take a second opinion. For how many days it was underwater? Even i faced the same situation during 2015 chennai flood. My bike was submerged in water for 4 to 5 days and in the workshop untouched for a week. The estimate i got was around rs 40,000. Later i spoke to an advisor (Arvind of souther motors chennai) who was very kind hearted and helped me. What he did was changed engine oil( free from royal enfield for flood affected vehicles), run the vehicle in idle for some time, changed engine oil again and this process repeated for 3 to 4 time. My final bill was around some 5000 out of which more than half was for electrical work. By the grace of almightly, My ds500 is running strong still.