Board Thread:Theories and Speculation/@comment-43776375-20190915194614/@comment-9782468-20190915220417

All the chakra from Shadow Clones return. However, keep in mind:

Not many people in Naruto do jutsu with 100% efficiency. So in making a Shadow Clone, some chakra is wasted for most people. And that effect is compounded the more Shadow Clones are made. Naruto originally dealt with it by using his massive reserves, but now he's actually just really good at the tech.

Naruto would not become a frog if his reserves were low and he obtained Sage chakra. This is because Sage chakra is already balanced with regular chakra. He would turn into a frog if he received an influx of Nature Energy, since he wouldn't have enough chakra to balance it out into Sage chakra.

If the clone became a frog, I think the clone would just be lost to Naruto and that SHadow Clones chakra would be gone, leaving Naruto to recuperate the lost chakra naturally.