This sounds like you were trying to perform the drag and drop on a workstation that was not the same as the one where these files were checked out. Or possibly the files were checked out, but a "Get Version" was performed such that it reverted to the last checked-in version in the vault.
Are either of these the case?
EPDM is going to copy out the files that are in the local cache. If you have modified versions of these files in your local cache, then that is what will be copied. If the files are checked out on a different machine, then the files in the local cache will be the latest ones on the server, assuming a "Get Latest" has been performed.