Hi,
Some days ago it was also happen with my site also. I could not found any backlinks and search query data, but tomorrow it is surprising i get my all data in webmater so don't worry about it. Please read that link It just say "No Data Available". You can find solution for your query. You specified that you have submitted new sitemap so now when Google crawl your site-map you get all data back. Google analytics data might be seems different because of these reasons.
"Google has not crawled your site since the changes were last made,
Google Analytics, track traffic only from users who have enabled JavaScript in their browser.
Webmaster Tools does some additional data processing - for example, to eliminate duplicates and visits from robots. "