He didnt go back "good" in Transference. The line of whether he was bad or good started to go gray after that but he was still partly dark after that. Hell he freaking was the proximate cause of Pa Kent's death after throwing down with him in the barn in Season 5.
I'd say that Lionel wasnt without a doubt good until about the end of Season 5 during Cyborg when he uttered the now infamous "You're secret is safe with me, Kal-El" line.
No, he does what he think is necessary to prevent Lex & the Teagues from discovering that those crystals are connected to Clark . So he plays both sides pretending to be his former evil self .
When he was downloaded with kryptonian knowledge by the water crystal Jor-El found Lionel to be worthy of being his Kryptonian vessel and a mentor to his son Kal-El .
Sometime after his return in season 6, Lionel made contact with J'onn J'onzz and they worked together in secret. Lionel pasted on the info Lana had gotten from Lex about the phantom Bizarro to Martian Manhunter who was tracking the phantom, While watching Clark from a distance .
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