Well, here we are at the crux of the problem where I am currently. I won't bore you with that so...
No, I would not look to change existing users. I would say let them stay until the are turned over by attrition. New users coming in would use their EmpID. AD and HR would be the 'systems of record', enhancing each other and have the other systems controlled by an IDM using the HR/AD tandem as its source.
Clearly, we have more to do than change a user ID. The overall design needs to be addressed first. Without clean data to rely on, any change will just carry over the original issues as pointed out by Julius.
I also agree with Martin, despite what our functional teams say, users will get used to numbers instead of alpha IDs.
Thank you both for your replies.