Why was only one of the subfolders was verified, and not the whole folder?

When dragging a folder onto Checkpoint, it will scan the folder for Media Hash Lists (MHL, extension .mhl). MHLs are created by offload software like Hedge, Silverstack, and Yoyotta. The MHL contains information about the files that were transferred, like name, size, and checksum. Only the files that end up in the MHL have checksums, and thus will be verified by Checkpoint.

To prevent this, create MHLs for the non-referenced files. Drag the subfolder that doesn't have a MHL onto Checkpoint and press "Create MHL". This will result in a complete MHL, so that the next time the whole folder can be verified by Checkpoint.