Hi Arkesh,
Bugs can occur in any system and PI is no exception. However, looking at the issue faced by you, I have seen a similar case where the object version was showing as different but at run-time it worked fine. The object did exists in the cache.As we usually do, cache was to be blamed.
Check if there are any conflicts in the system. Sometimes, locked objects if transported creates these kind of issues.
Try to run a dummy unit test in production ESR after you have imported the message mapping TR mapping Employee id field and see if it gets populated.
A new TR is always an option.
Ambrish