While i am riding my bicycle I hear a grinding noise at certain gears at my Scott Sub Cross 10. When it is in high gear ( at largest wheel at the front derailleur and at the smallest wheel at the rear derailleur) I hear such grinding noise and it feels also uneasy at the pedals. Not pedaling smoothly. This happened after I took the rear tire out for installing the kickstand. The bicycle is new so I assume there is no fundamental problem. My guess is I disrupted the adjustment of the rear derailleur. I tried indexing after watching a park tool video about it. It decreased the problem (now i hear the noise of grinding just at the last three gears). But problem not totally solved. if I keep riding the bike while avoiding the problematic gears, would it be totally fine? and what would you suggest, trying indexing again and then adjusting the whole rear gear?

New bikes have cable-stretch, that's typical. Limit screw may need adjustment. Double check that wheel axle is correct in drop-outs. Make sure wheel is aligned by sticking fingers in gap between seat-stays and tire. New bike? Should be no 'aggravated' noise. If the mechanicals are a tad confusing, take it by the LBS and make that bike happy again.

If there was no such noise before the kickstand installation it is likely that you misaligned the wheel when reinstalling it. However, it might be also due other reasons. Going by your description, it sounds like the chain is rubbing on the front derailleur cage, in which case the front derailleur needs adjusting.

The Scott Sub Cross 10 appears to have vertical rear dropouts, making a wheel alignment issue so bad that it impacts the drivetrain somewhat unlikely. It sounds like a trip to the bike shop to have them sort it may be worth your time. It may be a cable adjustment issue.