Basic file permissions might make it over such as read only and others but since it's between systems, ACL (access control lists) which are not part of a file's "permissions" will not.
I see nothing broken about that. File system permissions (ACL) are server/host specific and would have to be worked out per job.
-> IF you must copy such then do so in an OFFLINE mode. Here's how I do that. I boot up another OS and copy the files out since any OS restrictions or apps that have a lock on said file are now inactive.
-> copying an open file is easy. I do this all the time. I boot some Linux from an USB stick and copy the files over. No locks to contend with as the Windows OS is not running.
- > for the long pathname issue , you can just shorten the pathname if you can and if these are low paths , but if its as you post (over 600 path ) , you can use any of the third party tools that can handle this issue like the *SPAM* or Gs Richcopy 360 .
and for your info , you can use the second tool to handle all your problems which listed on the post