I've read that you do need to be careful with partial battery replacements. Even though the batteries are in separate banks they will charge as one bank anytime the ACR closes (assuming you have ACRs). While two batteries may be shot, the other two may only be marginally "ok". I would check the specific gravity of the electrolyte in each cell of each battery you intent to keep and do a thorough load test on each battery to get a more accurate picture of the health of the ones you plan to keep.
The risk you take as I understand it (imperfect as it is) is when your marginal batteries are combined with the new batteries for charging, you end up over charging the new ones to bring all the batteries up to full charge (as one temporary bank). What ends up happening is that the new batteries wear faster than they would than if you replaced all the batteries at once.
I believe the process goes something like this: the charger looks at overall voltage (when ACRs combine the batteries into a single bank after sensing a charging voltage) to know how much charge to input, not the voltage of each individual battery. If the charger output is 21 amps, all batteries will get 21 amps. So the newer batteries with a lower resistance will take the charge faster, and "fill up" before the older ones that have more resistance from longer use. At this point the charger is still looking at total volts for the combined batteries which will indicate more charge is still needed because the older batteries still aren’t full. Charging in the newer batteries will continue (because of ACRs being closed) to a level that they get overcharged and damaged over time because the older ones take longer to reach a full charge.
There are other Tugnuts I am sure that can add a more precise explanation. HTH, GF