If your site SEO was affected, you were most likely engaged in negative practices. Incoming Links do not calculate the same as they used to calculate, but do not think they are any less popular or affective in SEO.
Incoming Links and Links inside your site are still popular, but do not concentrate so much on how to manipulate Search Engines. Write unique content and provide informative posts and link to information that is important to readers. It is all about content that is beneficial to readers and it has to be Unique.
So many websites try to get hundreds of inbound links to their site in the hope it will put them on the first page of Google. You have to build links over time from sites that find your information informative. Random links mean nothing. It has to be links from sites that are providing additional information to their readers.
So, for site SEO, write unique content and provide linked content for your readers. You will build links over time and this is the best way to provide SEO for your site. Unique content over a period of time! Do not try writing for search engines if you care about SEO. Write for readers and search engines will follow, trust me!