Hi Shane thanks for posting in the Lucid Community! 

Lucid chart does not transfer deleted files to other users the message is most likely showing because the documents were previously shared with other users. 

If any of the documents transferred were Shared Documents the user you have transferred the files to will need to login to their Lucid account open the folder containing the transferred docs and duplicate or make a copy of these files to transfer ownership. The copy will show up in the account under "My Documents" and the owner of the new copy will be the current account. If the original document is shared with anyone else they will need to reshare the copy.

Hope this helps! If you have additional questions feel free to reply in this thread.

To make sure I understand you're saying the documents that have "This file has been deleted by the owner please make a copy of this file if you'd like to keep it" is a document that was shared by the orginal owner with the person who's account was transferred? 

It can be one of the causes for this message! The warning "This file has been deleted by the owner please make a copy of this file if you'd like to keep it" can be caused by a variety of issues when transferring documents and ownership of documents between users most of them pertaining to sharing. If the user is receiving this message they will want to make a duplicate/copy and ensure it is reshared with the previous users of the original document. 

If you would like I can open a support ticket so we can take a closer look at the specific documents within the account!