With quite a lot of commercial flight operations using the airline flight numbers these days for radio comms, the problems may be more likely administrative rather than operational.
Adding another letter on the end of the existing three letter suffix seems a reasonable solution. The British and the French operate thusly - and have done so for years - so any potential issues there would seem to have been resolved to the satisfaction of all parties. Where ops require aircraft identification by rego rather than flight number (or military designation), more precise radio procedures may be required, and everyone needs to be alert for the possibility of potential errors, but surely we are up to that. The expansion of data base requirements at all levels to fit the extra character needed could be something of a challenge, but we came through Y2K pretty well unscathed. In any event - we already have RAAus aircraft in the operational mix using the 2+4 numerical combinations, so changes in the mainstream aviation system should be quite workable if and when they become essential.
Finally, from what read, I think ICAO may well need to be involved in any change anyway.