For some reason, the number of links submitted & indexed through sitemap keeps changing. Where as doing a Google search on the domain using advanced tools reveals all links in Google Index. Can anyone please advise on how to resolve this?
Your problem is a bit unclear. What exactly is the problem there? Changing in sitemap links is not unusual. So don't worry about it.
Sitemap submitted & indexed are the two different things. In webmaster tool you can see this and the pages which are already indexed in google are the older version of your website page which are already indexed...