indexed urls

Hi there, I have been facing from the last couple of weeks. Google removed my indexed URLs. Before few days Google removed my 30 indexed URLs, I thought it's a routine drill but again Google removed 20 than 40, I was unable to know why this happened. If anybody suggests me any idea what to do...

I have a site that's migrating and completely changing navigation. It has really good organic traffic so naturally I'm trying to be extra careful I don't screw that up. I want to make sure I get all the indexed pages and do a 301 redirect for each. I know you can pull the first 1000 listings...