I have this problem. When I save an email with the option "save as" from windows mail IT will print the current date without maintaining the mail by default, but if you drag the email with the mouse and loose it in a folder now. I'm trying to fix this with this, but, did not work:
1) the .eml files change to the present date when they are indexed by the search indexer; this is, a few seconds after creation. Thus, backup/restore/sync will not work properly, but indexing.
2) if you delete that mentioned registry key, then the indexing of .eml files no longer works, i.e. you cannot find them in a full-text search. However, backup works now.
3) it is unknown whether the other solution, proposed by alecamiga, to link .eml to thunderbird and write lock the files, does the same or works better.