Is it possible that in case a site is set in CF but the NS does not point to CF, system will automatically remove those sites from CF? E.g. after 2-3 months? In case yes, is it possible to somehow restore it or manual work should start over again?
That is correct, though Cloudflare usually drops the domain earlier than two months.
When Cloudflare drops a domain, it typically keeps the site configuration for a while and if you add the domain again, it may restore that. If it does not, then it dropped the whole thing and you will need to reconfigure it. But adding the domain is always possible.