Can RClone move just the files from within folders?

Strange request I know, but I’m having an issue where a piece of software is incorrectly detecting folders as empty and is deleting them whilst there are files still within.

If I can transfer just the loose files from within a folder then I can bypass this issue.

Is this possible?

Not sure I’m understanding what you want - can you give an example and I’ll see if I can help - thanks!