Some sites comes with redirectors or "beacons" for detecting user presence. Example i'm on site X page A and there i click on link to go on page B. But due marketing department this pass via HTTP redirector or pure HTTP (and there 301 redirect to HTTPS). Then this page B can be not indexed.
This mean that once you set sitewide 301 redirect to encrypted connection you must make few more steps:
- you must check all resources to pass via this encrypted channel. Images, CSS, JS - just anything.
- you must check canonical to be set to HTTPS
- you must check that link between pages to be also HTTPS
- you must see any 3rd party tools for encrypted connection. Can be analytics software or "tracking pixels" or heat maps or ads.
- you must check if outgoing links from your site can be via other sites with encryption. Can be Wikipedia, Moz, Google. Since everything there is already encrypted you will skip frustrating HTTPS -> HTTP -> HTTPS jump too.
So then your site can be indexed in HTTPS. It's tricky procedure with many traps.