The implication of discussion on this issue is that to preserve metadata on files and folders one must have same custom content type on both the source and destination libraries. I have done this and yet have the warning of losing the metadata, and if I go ahead and do the move in fact the properties do not show in the folder.
Other discussion seems to glom thru this and accept the loss of the custom metadata. I would much rather fix the issue and retain the metadata having invested quite a bit in making it happen in the first place... Any suggestions?