Naruto never lost Six Paths but is just low on bijuu power hence the reason his cloak changed back.Who said he lost 9 bijuu chakra? And he was still in RSM in VOTE2, that's why he could fly. He still has the 9 Bijuu chakra, just most of the chakra comes from Kurama since Kurama is the strongest Bijuu.
Six Paths Sage mode can be used without the cloak. It debuted in Naruto's base form. The slit in the eyes is Kurama's chakra mixed in as we all know. And the absence of pigmentation indicates a heightened Sage Mode.
In the Boruto movie he is using Six Paths+Kurama+His Chakra(Asura influenced).