I fear this could be the case. I have seen several problems with KNIME workflows and OneDrive. For once there seem to be limitations on the characters that can be used in OneDrive depending on the admin settings and the version (academic. etc seems to have different default settings). The workflows might work first but would later be corrupted - this might especially be true if you try to transfer data KNIME workflows via OneDrive.
One (not good) option could be to try and reconstruct the original names of the files and folders - but it might be you will have to rely on a backup.
I have used DropBox with KNIME without issue.