It shouldn't be a .lua file, but I assume that's just a typo.
I'm not experienced with large users.txt files, nor do I know why large users.txt files cause issues. However, on my server I have a users.txt file that is 17kb and I haven't noticed any players losing ranks.
The only other cause I can think of is you have some new addon or module that is screwing up the ranks. Have you installed any addons/modules recently?
Trimming your users.txt file can't hurt anything, so I would suggest trying it anyways. I replied to a thread where someone was asking how to remove users that are in a certain group
here. Just replace the "new" with the group name you wish to remove, surrounded in quotes. You'll need Notepad++ or some other text editor that supports finding and replacing with regex. If you're too lazy to do that, you can just follow Caustic's advice and delete the entire file, adding people back to their ranks as needed.
EDIT:
Now that I think about it, I'm a bit confused as to how you can have a 14kb users file without any sort of autopromotion. I have autopromote on my server, so everyone with 12 hours is added to a group. Unless you have a ton of VIP users, something is awry.