Making files available offline worked perfectly on my iPad Pro, but I had this issue with exactly the same folders/subfolders/files on my iPhone 7.
The download stalled after so many folders/files were completed, and would not refresh or re-start, for days.
22 files remaining.
Eventually I chose to 'Remove from Device', the whole containing folder, and immediately reselected to 'Make available offline'.
The remaining files then downloaded and my file collection is now complete and available offline.
I hope this might help.