I uploaded the game, but it wasn't indexed or verified (someone said it should be), but it immediately appeared on the site, that surprised me, but okay. 

•I published the game, but I didn't have the Developer's Diary, and now I have an update, and I'm wondering if I post it, will the site consider this update as the initial version or independent? 

I'm going to be at the top of the new game list or what?? 

•by the way, about updates. How long can a game update be, if I just partially changed the design or added small new features, does that count? If you edited the visual part but didn't add levels or something.

I'm going to be at the top of the new game list or what??

If you mark your devlog as Major Release or Update, itch.io staff will check it, and if it meets their criteria your game can be bumped up to the top of new releases again. Otherwise it's up to you how much you change every time.