I think to be able to help you it would be good to understand your process better.
Who gives a MRN to the patient?
I assume that each MRN should be given only once and it should identify a patient, no matter which site he/she is at, correct?
My suspicion is that this is rather a internal organization problem, then a problem with the survey it self. But I think we don't know enough about what you are doing, what the process is and how the MRNs work in your organization.
Help us to help you!
Provide your LS version and where it is installed (own server, uni/employer, SaaS hosting, etc.).
Always provide a LSS file (not LSQ or LSG).
Note: I answer at this forum in my spare time, I'm not a LimeSurvey GmbH employee.