I'm trying to understand the situation, if I guess wrongly please let me know.
A field instrument does not always live up to specifications, or during the life of the instrument certain procedures are found to produce good test results while perhaps the established protocol does not.
To change the protocol (because a new set of rules is needed to get the right result), first perform some tests using another instrument which is known to be accurate and comparing results of the field instrument (1) using the old protocol and the results (2) using the proposed new protocol. Write up the data, showing the new protocol which is necessary to produce the same results as the accurate instrument. Then list the rules or steps involved in the new protocol.
Submit the document to your boss and coworkers for everybody's agreement and the new protocol may then be adopted for that field instrument.
It is not a simple matter to change the protocol (I presume you are taling about the communications protocol being used). Your control system might not be able to handle the new bus system you propose or the type of bus system you want to use might not be suitable or allowed in the area if it is intrinsic safe.
Why would you want to change your bus system?
The first step would be to frind out whether your proposed bus system is even allowed for the area that you want to install it in.
Then you need to find out if there is a communications processor for your control system that would handle the bus type you want to move to.
Then ......
I am not going to go into detail about finding out manufacturers specifications and wiring details - but as you can see it is no simple matter.